Variant report

Variant	rs10946940
Chromosome Location	chr6:27560587-27560588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:295)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:295 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr6:27560222-27560889	GM12878	blood:	n/a	n/a
2	GABPA	chr6:27560564-27560729	Hela-S3	cervix:	n/a	n/a
3	TBL1XR1	chr6:27560261-27560914	K562	blood:	n/a	n/a
4	PML	chr6:27560120-27561014	GM12878	blood:	n/a	n/a
5	RFX5	chr6:27560379-27560787	Hela-S3	cervix:	n/a	n/a
6	EP300	chr6:27560292-27560837	GM12878	blood:	n/a	n/a
7	RXRA	chr6:27560467-27560742	GM12878	blood:	n/a	n/a
8	TEAD4	chr6:27560254-27560936	ECC-1	luminal epithelium:	n/a	n/a
9	YY1	chr6:27560464-27560799	A549	lung:	n/a	n/a
10	HMGN3	chr6:27560207-27560775	K562	blood:	n/a	n/a
11	CTCF	chr6:27560460-27560610	GM12873	blood:	n/a	n/a
12	TCF12	chr6:27560485-27560814	GM12878	blood:	n/a	n/a
13	FOSL2	chr6:27560370-27560833	HepG2	liver:	n/a	n/a
14	ELF1	chr6:27560361-27560819	HepG2	liver:	n/a	n/a
15	FOXA2	chr6:27560359-27560850	HepG2	liver:	n/a	n/a
16	ZNF143	chr6:27560484-27560791	Hela-S3	cervix:	n/a	n/a
17	BHLHE40	chr6:27560016-27560994	K562	blood:	n/a	n/a
18	POLR2A	chr6:27560446-27560705	GM12878	blood:	n/a	n/a
19	REST	chr6:27560076-27560941	K562	blood:	n/a	n/a
20	CTCF	chr6:27560540-27560690	SK-N-SH_RA	brain:	n/a	n/a
21	POLR2A	chr6:27559682-27561420	H1-neurons	neurons:	n/a	n/a
22	SPI1	chr6:27560486-27560761	GM12878	blood:	n/a	n/a
23	MYC	chr6:27560582-27560727	MCF-7	breast:	n/a	n/a
24	REST	chr6:27560462-27560862	HL-60	blood:	n/a	n/a
25	RUNX3	chr6:27560261-27560834	GM12878	blood:	n/a	n/a
26	SIN3AK20	chr6:27560496-27560735	HepG2	liver:	n/a	n/a
27	RPC155	chr6:27560186-27560885	Hela-S3	cervix:	n/a	n/a
28	SIN3A	chr6:27559517-27561282	H1-hESC	embryonic stem cell:	n/a	chr6:27561096-27561109
29	REST	chr6:27560418-27560924	HepG2	liver:	n/a	n/a
30	ELF1	chr6:27560231-27560799	HepG2	liver:	n/a	n/a
31	MYC	chr6:27560329-27560758	MCF10A-Er-Src	breast:	n/a	n/a
32	REST	chr6:27560505-27560925	Hela-S3	cervix:	n/a	n/a
33	SIX5	chr6:27560421-27560728	K562	blood:	n/a	n/a
34	CTCF	chr6:27560513-27560846	A549	lung:	n/a	n/a
35	ELF1	chr6:27560290-27560695	K562	blood:	n/a	n/a
36	TCF3	chr6:27560523-27560728	GM12878	blood:	n/a	n/a
37	MYC	chr6:27560366-27560845	K562	blood:	n/a	n/a
38	JUN	chr6:27560134-27560870	K562	blood:	n/a	n/a
39	SIN3AK20	chr6:27560472-27560849	H1-hESC	embryonic stem cell:	n/a	n/a
40	BRCA1	chr6:27560404-27560971	H1-hESC	embryonic stem cell:	n/a	n/a
41	SPI1	chr6:27560500-27560756	K562	blood:	n/a	n/a
42	ETS1	chr6:27560388-27560842	A549	lung:	n/a	chr6:27560437-27560444
43	REST	chr6:27560282-27561113	A549	lung:	n/a	chr6:27561096-27561105
44	MAX	chr6:27560287-27560870	K562	blood:	n/a	n/a
45	YY1	chr6:27560450-27560751	GM12892	blood:	n/a	n/a
46	CCNT2	chr6:27560140-27560939	K562	blood:	n/a	chr6:27560689-27560709
47	TCF12	chr6:27560510-27560827	H1-hESC	embryonic stem cell:	n/a	n/a
48	REST	chr6:27560446-27560931	H1-hESC	embryonic stem cell:	n/a	n/a
49	SMC3	chr6:27560378-27560973	HepG2	liver:	n/a	n/a
50	ATF3	chr6:27559169-27561107	A549	lung:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27558513..27562026-chr6:27562388..27564787,3	K562	blood:
2	chr6:27485761..27488358-chr6:27559045..27561077,2	K562	blood:
3	chr6:27531650..27535233-chr6:27560375..27562860,3	K562	blood:
4	chr6:27532623..27535233-chr6:27560375..27562747,2	K562	blood:
5	chr6:27516649..27519121-chr6:27558606..27561383,2	K562	blood:
6	chr6:27549818..27556949-chr6:27557615..27563432,7	K562	blood:
7	chr6:27549715..27554180-chr6:27555593..27563261,8	K562	blood:
8	chr6:27560152..27562900-chr6:28715549..28717321,2	K562	blood:
9	chr6:27558583..27561214-chr6:27719565..27721812,2	K562	blood:
10	chr6:27559085..27561066-chr6:27755940..27758239,2	K562	blood:
11	chr6:27558513..27561961-chr6:27562522..27566444,4	K562	blood:
12	chr6:27559025..27560718-chr6:27653331..27656285,2	K562	blood:
13	chr6:27513701..27516143-chr6:27559137..27561028,2	K562	blood:

No data

Variant related genes	Relation type
RNU6-471P	TF binding region
ENSG00000206671	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1022486	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1033451	0.82[ASN][1000 genomes]
rs10807026	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10807029	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10946935	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[EUR][1000 genomes]
rs10946936	0.86[EUR][1000 genomes]
rs10946938	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12197514	0.83[ASN][1000 genomes]
rs12208078	0.85[EUR][1000 genomes]
rs12215012	0.86[EUR][1000 genomes]
rs13201411	0.86[EUR][1000 genomes]
rs2056924	0.87[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2064093	0.86[LWK][hapmap];0.80[YRI][hapmap]
rs2294480	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2294481	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2393964	0.81[YRI][hapmap]
rs4272217	0.90[ASN][1000 genomes]
rs4713112	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713113	0.93[ASN][1000 genomes]
rs4713120	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs62401383	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67734963	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6899903	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6908295	0.88[ASN][1000 genomes]
rs6915266	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6915987	0.83[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6916878	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6918038	0.90[ASN][1000 genomes]
rs6921256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6933926	0.87[ASN][1000 genomes]
rs6934437	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6934794	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7761966	0.86[LWK][hapmap];0.81[YRI][hapmap]
rs7764081	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7769662	0.94[ASN][1000 genomes]
rs7774939	0.93[ASN][1000 genomes]
rs7775817	0.94[ASN][1000 genomes]
rs9295747	0.84[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.90[MKK][hapmap]
rs9348772	0.81[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];0.96[YRI][hapmap]
rs9357042	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366697	0.81[EUR][1000 genomes]
rs9380007	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs9393830	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9393831	0.83[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs9468156	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systemic lupus erythematosus	24871463	GWAS catalog

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10946940	HIST1H3D	cis	parietal	SCAN
rs10946940	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs10946940	HIST1H3C	cis	cerebellum	SCAN
rs10946940	ZNF192	cis	parietal	SCAN
rs10946940	BTN3A3	cis	parietal	SCAN
rs10946940	BTN2A1	cis	parietal	SCAN
rs10946940	HIST1H2BE	cis	cerebellum	SCAN
rs10946940	AL022393.7	cis	Muscle Skeletal	GTEx
rs10946940	BTN3A3	cis	cerebellum	SCAN
rs10946940	ZNF204P	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27559200-27560800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:27559200-27560800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:27559400-27560800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:27559400-27560800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:27559400-27560800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr6:27559400-27560800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:27559400-27560800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
8	chr6:27559400-27560800	Active TSS	K562	blood
9	chr6:27559400-27561000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:27559400-27561200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:27559400-27561200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:27559600-27560600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:27559600-27560600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
14	chr6:27559600-27560600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:27559600-27560600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
16	chr6:27559600-27560600	Active TSS	GM12878-XiMat	blood
17	chr6:27559600-27560800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:27559600-27560800	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:27559600-27560800	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr6:27559600-27560800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:27559600-27560800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:27559600-27560800	Flanking Active TSS	HUVEC	blood vessel
23	chr6:27559600-27561000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:27559600-27561000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:27559600-27561000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:27559600-27561000	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr6:27559600-27561000	Active TSS	NH-A	brain
28	chr6:27559600-27561200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:27559600-27561400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:27559600-27561400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:27559600-27561400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:27559600-27561600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
33	chr6:27559600-27561600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:27559600-27561800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:27559600-27562000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:27559600-27562200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:27559600-27562200	Active TSS	A549	lung
38	chr6:27559600-27562600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:27559600-27562800	Active TSS	H9 Cell Line	embryonic stem cell
40	chr6:27559800-27560600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:27559800-27560600	Active TSS	Placenta	Placenta
42	chr6:27559800-27560600	Active TSS	Placenta Amnion	Placenta Amnion
43	chr6:27559800-27560800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
44	chr6:27559800-27560800	Bivalent/Poised TSS	Fetal Lung	lung
45	chr6:27559800-27560800	Active TSS	HSMMtube	muscle
46	chr6:27559800-27561000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:27559800-27561000	Active TSS	NHDF-Ad	bronchial
48	chr6:27559800-27561200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
49	chr6:27559800-27561200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr6:27559800-27561400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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