Variant report

Variant	rs17619838
Chromosome Location	chr6:15313353-15313354
allele	A/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	POLR2A	chr6:15313240-15313763	GM12892	blood:	n/a	n/a
2	POLR2A	chr6:15313088-15313996	GM12878	blood:	n/a	n/a
3	STAT5A	chr6:15312693-15313989	GM12878	blood:	n/a	chr6:15313922-15313929 chr6:15313734-15313742 chr6:15313211-15313231
4	POLR2A	chr6:15313291-15313675	GM12892	blood:	n/a	n/a
5	MTA3	chr6:15312725-15314004	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:15312645-15314261	GM12878	blood:	n/a	n/a
7	MTA3	chr6:15312480-15314109	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:15312487-15314519	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:15313167-15314020	GM18505	blood:	n/a	n/a
10	POLR2A	chr6:15313321-15313870	GM12891	blood:	n/a	n/a
11	POLR2A	chr6:15313303-15313925	GM12891	blood:	n/a	n/a
12	POLR2A	chr6:15313234-15314014	GM12891	blood:	n/a	n/a
13	PML	chr6:15312615-15314127	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:15312704-15314473	GM12891	blood:	n/a	n/a
15	POLR2A	chr6:15313222-15313959	GM12892	blood:	n/a	n/a
16	WRNIP1	chr6:15312725-15313875	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:15313118-15313929	GM12892	blood:	n/a	n/a
18	POLR2A	chr6:15313328-15313963	GM12891	blood:	n/a	n/a
19	POLR2A	chr6:15313305-15313889	Raji	blood:	n/a	n/a
20	IKZF1	chr6:15312722-15313499	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15248268..15250202-chr6:15310561..15313367,2	K562	blood:
2	chr6:15310524..15313443-chr6:15327959..15329867,2	K562	blood:

Variant related genes	Relation type
RNU6-522P	TF binding region
ENSG00000008083	Chromatin interaction
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10949291	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10949292	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10949293	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10949294	1.00[CHB][hapmap]
rs10949295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11759040	1.00[JPT][hapmap]
rs11759478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs11759828	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11759847	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12192599	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12198692	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12198694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12201889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204124	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12205420	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12206745	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12209228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209453	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209539	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12209748	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210592	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211278	1.00[CHB][hapmap]
rs12211777	0.84[EUR][1000 genomes]
rs12212013	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214719	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12215596	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215740	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192347	1.00[CHB][hapmap]
rs13194410	1.00[CHB][hapmap]
rs13205396	1.00[CHB][hapmap]
rs13205612	1.00[CHB][hapmap]
rs16876250	0.84[EUR][1000 genomes]
rs16876278	1.00[CHB][hapmap]
rs17575737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs17576233	1.00[CHB][hapmap]
rs17576436	1.00[CHB][hapmap]
rs17619730	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17637773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17638192	1.00[CHB][hapmap]
rs17638720	1.00[ASW][hapmap]
rs17687211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17713010	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55634912	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55980198	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902997	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6919296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6935879	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6938919	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72834551	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72834590	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7765425	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs794775	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538144	chr6:15310696-15364984	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15301200-15313400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:15305200-15313600	Weak transcription	Liver	Liver
3	chr6:15306000-15318600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:15307000-15314800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:15307400-15314400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:15307600-15314000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:15308800-15314800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:15309200-15320600	Weak transcription	A549	lung
9	chr6:15310200-15318200	Weak transcription	Fetal Kidney	kidney
10	chr6:15310600-15315000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr6:15311000-15314600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr6:15311000-15315200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:15311000-15322200	Weak transcription	Fetal Intestine Small	intestine
14	chr6:15311200-15313600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:15311200-15313600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:15311200-15314400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr6:15311200-15317600	Weak transcription	Stomach Mucosa	stomach
18	chr6:15311200-15330600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:15311600-15313400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:15311600-15313400	Weak transcription	Aorta	Aorta
21	chr6:15311800-15313400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr6:15311800-15314400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:15311800-15314600	Enhancers	Primary B cells from peripheral blood	blood
24	chr6:15311800-15315200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:15312000-15314200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:15312000-15314400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr6:15312000-15314400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:15312200-15314000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr6:15312200-15314000	Enhancers	HUVEC	blood vessel
30	chr6:15312200-15314200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr6:15312200-15314400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:15312200-15314600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:15312200-15315000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:15312200-15317400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr6:15312400-15313400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:15312400-15313800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:15312400-15314000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:15312400-15314000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:15312400-15314000	Enhancers	Stomach Smooth Muscle	stomach
40	chr6:15312400-15314200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:15312400-15314400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:15312400-15314400	Enhancers	Small Intestine	intestine
43	chr6:15312400-15314600	Enhancers	Fetal Thymus	thymus
44	chr6:15312400-15315000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:15312400-15315800	Enhancers	Primary hematopoietic stem cells	blood
46	chr6:15312600-15313400	Enhancers	Osteobl	bone
47	chr6:15312600-15313600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:15312600-15313800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr6:15312600-15313800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:15312600-15313800	Enhancers	NHEK	skin

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