Variant report

Variant	rs3115572
Chromosome Location	chr6:32220484-32220485
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr6:32220393-32220713	GM12878	blood:	n/a	n/a
2	SPI1	chr6:32220472-32220719	K562	blood:	n/a	n/a
3	SPI1	chr6:32220377-32220750	HL-60	blood:	n/a	n/a
4	SPI1	chr6:32220360-32220812	HL-60	blood:	n/a	n/a
5	EP300	chr6:32220453-32220717	GM12878	blood:	n/a	n/a
6	SPI1	chr6:32220308-32220723	GM12891	blood:	n/a	n/a
7	SPI1	chr6:32220353-32220799	GM12891	blood:	n/a	n/a
8	SPI1	chr6:32220464-32220691	GM12878	blood:	n/a	n/a
9	RUNX3	chr6:32220417-32220785	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000225914	TF binding region

Extended variants
information (count: 148 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1559872	0.81[ASN][1000 genomes]
rs1559873	0.88[ASN][1000 genomes]
rs1559874	0.88[ASN][1000 genomes]
rs2114434	0.81[ASN][1000 genomes]
rs2114435	0.88[ASN][1000 genomes]
rs3096668	0.81[ASN][1000 genomes]
rs3096669	0.82[ASN][1000 genomes]
rs3096672	0.88[ASN][1000 genomes]
rs3096673	0.81[ASN][1000 genomes]
rs3096674	0.88[ASN][1000 genomes]
rs3096675	0.81[ASN][1000 genomes]
rs3096676	0.81[ASN][1000 genomes]
rs3096677	0.88[ASN][1000 genomes]
rs3096678	0.88[ASN][1000 genomes]
rs3096679	0.81[ASN][1000 genomes]
rs3096680	0.81[ASN][1000 genomes]
rs3096681	0.81[ASN][1000 genomes]
rs3096684	0.88[ASN][1000 genomes]
rs3096686	0.81[ASN][1000 genomes]
rs3096687	0.83[ASN][1000 genomes]
rs3096700	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3115552	0.81[ASN][1000 genomes]
rs3115553	0.81[ASN][1000 genomes]
rs3115557	0.87[ASN][1000 genomes]
rs3115558	0.88[ASN][1000 genomes]
rs3115559	0.81[ASN][1000 genomes]
rs3115560	0.81[ASN][1000 genomes]
rs3115561	0.81[ASN][1000 genomes]
rs3115563	0.81[ASN][1000 genomes]
rs3115564	0.86[ASN][1000 genomes]
rs3115565	0.88[ASN][1000 genomes]
rs3115566	0.81[ASN][1000 genomes]
rs3115567	0.90[ASN][1000 genomes]
rs3115568	0.85[ASN][1000 genomes]
rs3115569	0.85[ASN][1000 genomes]
rs3115571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130309	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130316	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130320	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130321	0.91[ASN][1000 genomes]
rs3130322	0.85[ASN][1000 genomes]
rs3130327	0.81[ASN][1000 genomes]
rs3130329	0.81[ASN][1000 genomes]
rs3130330	0.81[ASN][1000 genomes]
rs3130331	0.88[ASN][1000 genomes]
rs3130332	0.81[ASN][1000 genomes]
rs3130333	0.81[ASN][1000 genomes]
rs3130335	0.81[ASN][1000 genomes]
rs3130336	0.88[ASN][1000 genomes]
rs3130337	0.88[ASN][1000 genomes]
rs3130340	0.81[ASN][1000 genomes]
rs3130341	0.80[ASN][1000 genomes]
rs3132926	0.81[ASN][1000 genomes]
rs3132927	0.88[ASN][1000 genomes]
rs3132928	0.81[ASN][1000 genomes]
rs3132929	0.81[ASN][1000 genomes]
rs3132930	0.81[ASN][1000 genomes]
rs3132931	0.88[ASN][1000 genomes]
rs3132932	0.81[ASN][1000 genomes]
rs3132945	0.81[ASN][1000 genomes]
rs3132966	0.91[ASN][1000 genomes]
rs3132967	0.85[ASN][1000 genomes]
rs3132970	0.81[ASN][1000 genomes]
rs3132972	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132973	0.80[ASN][1000 genomes]
rs3864301	0.82[ASN][1000 genomes]
rs6457513	0.85[ASN][1000 genomes]
rs6457514	0.85[ASN][1000 genomes]
rs6457515	0.85[ASN][1000 genomes]
rs6457516	0.85[ASN][1000 genomes]
rs6457526	0.81[ASN][1000 genomes]
rs6908927	0.83[ASN][1000 genomes]
rs6915879	0.82[ASN][1000 genomes]
rs6927529	0.86[ASN][1000 genomes]
rs6927856	0.86[ASN][1000 genomes]
rs6934776	0.82[ASN][1000 genomes]
rs6939410	0.82[ASN][1000 genomes]
rs7746994	0.81[ASN][1000 genomes]
rs7749824	0.81[ASN][1000 genomes]
rs7750783	0.82[ASN][1000 genomes]
rs7757711	0.86[ASN][1000 genomes]
rs7758030	0.86[ASN][1000 genomes]
rs7765103	0.81[ASN][1000 genomes]
rs7765109	0.81[ASN][1000 genomes]
rs7767325	0.81[ASN][1000 genomes]
rs7770017	0.83[ASN][1000 genomes]
rs9267972	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9268012	0.85[ASN][1000 genomes]
rs9268013	0.92[ASN][1000 genomes]
rs9268014	0.85[ASN][1000 genomes]
rs9268015	0.85[ASN][1000 genomes]
rs9268016	0.85[ASN][1000 genomes]
rs9268017	0.85[ASN][1000 genomes]
rs9268018	0.81[ASN][1000 genomes]
rs9268025	0.81[ASN][1000 genomes]
rs9268029	0.84[ASN][1000 genomes]
rs9268030	0.83[ASN][1000 genomes]
rs9268031	0.83[ASN][1000 genomes]
rs9268055	0.81[ASN][1000 genomes]
rs9268056	0.81[ASN][1000 genomes]
rs9268057	0.81[ASN][1000 genomes]
rs9268059	0.88[ASN][1000 genomes]
rs9268074	0.81[ASN][1000 genomes]
rs9268076	0.80[ASN][1000 genomes]
rs9268083	0.82[ASN][1000 genomes]
rs9268096	0.88[ASN][1000 genomes]
rs9268142	0.86[ASN][1000 genomes]
rs9268176	0.82[ASN][1000 genomes]
rs9268179	0.80[ASN][1000 genomes]
rs9268180	0.82[ASN][1000 genomes]
rs9268182	0.82[ASN][1000 genomes]
rs9268191	0.82[ASN][1000 genomes]
rs9268194	0.82[ASN][1000 genomes]
rs9268197	0.82[ASN][1000 genomes]
rs9268202	0.82[ASN][1000 genomes]
rs9268207	0.81[ASN][1000 genomes]
rs9268212	0.82[ASN][1000 genomes]
rs9268222	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv601950	chr6:31785438-32492308	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
3	nsv601951	chr6:31785438-32496748	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
4	nsv601955	chr6:31785453-32484368	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
5	nsv601956	chr6:31785453-32492308	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
6	nsv601961	chr6:31868322-32484368	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	nsv601972	chr6:31947594-32484368	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv601975	chr6:31949352-32484368	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv601976	chr6:31949352-32508887	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv601977	chr6:31949352-32651056	Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
11	nsv601980	chr6:31950266-32484368	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
12	nsv601982	chr6:31951207-32484368	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
13	nsv601983	chr6:31951367-32484368	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv601984	chr6:31951912-32484368	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
15	nsv601999	chr6:31952422-32484368	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
16	nsv602000	chr6:31952422-32552416	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
17	nsv602015	chr6:31953467-32481507	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
18	nsv602016	chr6:31953467-32484368	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
19	nsv602017	chr6:31953467-32505730	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
20	nsv602018	chr6:31953467-32509985	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
21	nsv602019	chr6:31953467-32779803	Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
22	nsv602029	chr6:31955572-32484368	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
23	nsv602035	chr6:31959480-32484368	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
24	nsv602036	chr6:31959878-32484368	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
25	nsv602052	chr6:31972034-32481507	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
26	nsv602053	chr6:31972034-32484368	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
27	nsv602054	chr6:31972034-32779803	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
28	nsv602086	chr6:31986320-32484368	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
29	nsv1024599	chr6:32007556-32481240	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
30	nsv1028682	chr6:32194392-32233814	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3115572	HLA-DRA	cis	multi-tissue	Pritchard
rs3115572	HLA-DRB5	cis	parietal	SCAN
rs3115572	HLA-DRB5	cis	multi-tissue	Pritchard
rs3115572	HLA-C	cis	multi-tissue	Pritchard
rs3115572	HLA-DRB5	cis	lymphoblastoid	GTEx
rs3115572	HLA-DQA2	cis	lymphoblastoid	seeQTL
rs3115572	HLA-DRB5	cis	cerebellum	SCAN
rs3115572	GRM4	cis	cerebellum	SCAN
rs3115572	C6orf227	cis	cerebellum	SCAN
rs3115572	ERG	trans	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:32213200-32222400	Weak transcription	Thymus	Thymus
2	chr6:32213200-32222600	Weak transcription	Fetal Thymus	thymus
3	chr6:32217200-32222600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:32217400-32222000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:32219800-32220600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:32220000-32220800	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:32220000-32220800	Enhancers	GM12878-XiMat	blood
8	chr6:32220000-32221200	Enhancers	Primary B cells from cord blood	blood
9	chr6:32220200-32220600	Enhancers	NHEK	skin
10	chr6:32220200-32220800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:32220200-32220800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:32220200-32220800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:32220200-32220800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr6:32220200-32220800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:32220200-32221000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:32220200-32221000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:32220200-32221000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:32220200-32221000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:32220200-32221000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:32220200-32221000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr6:32220200-32222800	Enhancers	HUVEC	blood vessel
22	chr6:32220400-32220600	Enhancers	H9 Cell Line	embryonic stem cell
23	chr6:32220400-32220600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr6:32220400-32220600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:32220400-32220600	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr6:32220400-32220800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr6:32220400-32221000	Enhancers	Primary T cells from cord blood	blood
28	chr6:32220400-32222600	Weak transcription	Hela-S3	cervix

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