Variant report

Variant	rs3802967
Chromosome Location	chr11:18344064-18344065
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	REST	chr11:18343090-18344327	HL-60	blood:	n/a	chr11:18343576-18343586
2	SIN3AK20	chr11:18343439-18344288	SK-N-SH	brain:	n/a	n/a
3	SIN3AK20	chr11:18343480-18344334	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr11:18343358-18344750	Hela-S3	cervix:	n/a	chr11:18344699-18344706 chr11:18343795-18343804 chr11:18344068-18344077 chr11:18344067-18344078 chr11:18343795-18343804 chr11:18344101-18344110 chr11:18344100-18344111 chr11:18344099-18344112 chr11:18344699-18344708
5	FOS	chr11:18343513-18344204	HUVEC	blood vessel:	n/a	chr11:18343674-18343682 chr11:18344064-18344072 chr11:18343738-18343747
6	POLR2A	chr11:18343357-18344289	HCT-116	colon:	n/a	n/a
7	POLR2A	chr11:18343102-18344765	K562	blood:	n/a	n/a
8	YY1	chr11:18343547-18344264	K562	blood:	n/a	n/a
9	GTF2B	chr11:18343518-18344257	K562	blood:	n/a	n/a
10	HNF4G	chr11:18343516-18344202	HepG2	liver:	n/a	n/a
11	USF2	chr11:18343458-18344626	H1-hESC	embryonic stem cell:	n/a	chr11:18343789-18343810 chr11:18344099-18344112 chr11:18344067-18344076 chr11:18343793-18343806 chr11:18343795-18343804 chr11:18343793-18343804 chr11:18344068-18344077 chr11:18344101-18344110 chr11:18344100-18344109 chr11:18344062-18344083 chr11:18343796-18343805 chr11:18344102-18344111 chr11:18344068-18344077 chr11:18343795-18343804 chr11:18344069-18344078 chr11:18344171-18344187 chr11:18344101-18344110
12	USF2	chr11:18343592-18344300	K562	blood:	n/a	chr11:18343789-18343810 chr11:18344099-18344112 chr11:18344067-18344076 chr11:18343793-18343806 chr11:18343795-18343804 chr11:18343793-18343804 chr11:18344068-18344077 chr11:18344101-18344110 chr11:18344100-18344109 chr11:18344062-18344083 chr11:18343796-18343805 chr11:18344102-18344111 chr11:18344068-18344077 chr11:18343795-18343804 chr11:18344069-18344078 chr11:18344171-18344187 chr11:18344101-18344110
13	EGR1	chr11:18343522-18344238	K562	blood:	n/a	chr11:18343786-18343795
14	TEAD4	chr11:18343412-18344285	HepG2	liver:	n/a	n/a
15	PML	chr11:18342724-18344513	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:18343363-18344379	GM18526	blood:	n/a	n/a
17	USF1	chr11:18343470-18344265	A549	lung:	n/a	chr11:18343789-18343810 chr11:18344099-18344112 chr11:18344067-18344076 chr11:18343793-18343806 chr11:18343795-18343804 chr11:18344068-18344077 chr11:18344101-18344110 chr11:18344100-18344109 chr11:18344062-18344083 chr11:18343796-18343805 chr11:18344102-18344111 chr11:18344068-18344077 chr11:18343795-18343804 chr11:18344069-18344078 chr11:18344171-18344187 chr11:18344101-18344110
18	ELF1	chr11:18343562-18344310	HepG2	liver:	n/a	chr11:18344174-18344186
19	MYC	chr11:18343254-18344808	NB4	blood:	n/a	chr11:18344699-18344706 chr11:18343795-18343804 chr11:18343353-18343362 chr11:18344068-18344077 chr11:18344067-18344078 chr11:18343795-18343804 chr11:18344101-18344110 chr11:18344100-18344111 chr11:18344099-18344112 chr11:18344699-18344708
20	IRF1	chr11:18343148-18344309	K562	blood:	n/a	chr11:18343353-18343362 chr11:18343179-18343189 chr11:18343993-18344006 chr11:18343804-18343818
21	POLR2A	chr11:18343281-18344415	GM18951	blood:	n/a	n/a
22	E2F4	chr11:18343501-18344213	MCF10A-Er-Src	breast:	n/a	chr11:18343739-18343748 chr11:18343737-18343746
23	HNF4A	chr11:18343501-18344239	HepG2	liver:	n/a	n/a
24	CREB1	chr11:18343462-18344272	A549	lung:	n/a	chr11:18343736-18343749
25	TAF1	chr11:18343282-18344308	PFSK-1	brain:	n/a	n/a
26	SIN3AK20	chr11:18343226-18344509	MCF-7	breast:	n/a	n/a
27	POLR2A	chr11:18343388-18344482	H1-hESC	embryonic stem cell:	n/a	n/a
28	TBL1XR1	chr11:18342698-18344251	K562	blood:	n/a	n/a
29	TBP	chr11:18343154-18344310	HepG2	liver:	n/a	n/a
30	POLR2A	chr11:18343356-18344350	U87	brain:	n/a	n/a
31	TCF12	chr11:18343469-18344257	A549	lung:	n/a	n/a
32	YY1	chr11:18343492-18344263	HCT-116	colon:	n/a	n/a
33	POLR2A	chr11:18343375-18344398	HepG2	liver:	n/a	n/a
34	USF1	chr11:18343486-18344470	ECC-1	luminal epithelium:	n/a	chr11:18343789-18343810 chr11:18344099-18344112 chr11:18344067-18344076 chr11:18343793-18343806 chr11:18343795-18343804 chr11:18344068-18344077 chr11:18344101-18344110 chr11:18344100-18344109 chr11:18344062-18344083 chr11:18343796-18343805 chr11:18344102-18344111 chr11:18344068-18344077 chr11:18343795-18343804 chr11:18344069-18344078 chr11:18344171-18344187 chr11:18344101-18344110
35	GTF2F1	chr11:18343491-18344280	H1-hESC	embryonic stem cell:	n/a	n/a
36	EP300	chr11:18343490-18344251	SK-N-SH_RA	brain:	n/a	chr11:18344094-18344101
37	TAF1	chr11:18343362-18344402	ECC-1	luminal epithelium:	n/a	n/a
38	ZBTB33	chr11:18343392-18344287	A549	lung:	n/a	n/a
39	ZNF384	chr11:18343508-18344202	K562	blood:	n/a	n/a
40	USF1	chr11:18343477-18344390	H1-hESC	embryonic stem cell:	n/a	chr11:18343789-18343810 chr11:18344099-18344112 chr11:18344067-18344076 chr11:18343793-18343806 chr11:18343795-18343804 chr11:18344068-18344077 chr11:18344101-18344110 chr11:18344100-18344109 chr11:18344062-18344083 chr11:18343796-18343805 chr11:18344102-18344111 chr11:18344068-18344077 chr11:18343795-18343804 chr11:18344069-18344078 chr11:18344171-18344187 chr11:18344101-18344110
41	POLR2A	chr11:18343245-18344811	HepG2	liver:	n/a	n/a
42	FOS	chr11:18343462-18344271	K562	blood:	n/a	chr11:18343674-18343682 chr11:18344064-18344072 chr11:18343738-18343747
43	TAF1	chr11:18343392-18344281	K562	blood:	n/a	n/a
44	POLR2A	chr11:18343116-18344456	HL-60	blood:	n/a	n/a
45	JUN	chr11:18342893-18344315	K562	blood:	n/a	chr11:18343674-18343682 chr11:18344064-18344072 chr11:18343017-18343026 chr11:18343353-18343361 chr11:18343352-18343362 chr11:18343737-18343750 chr11:18343352-18343362 chr11:18343738-18343747
46	POLR2A	chr11:18343413-18344687	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr11:18343040-18344682	K562	blood:	n/a	n/a
48	MYBL2	chr11:18343384-18344279	HepG2	liver:	n/a	chr11:18343771-18343786
49	ELK4	chr11:18343264-18344276	Hela-S3	cervix:	n/a	chr11:18344093-18344102 chr11:18344094-18344102 chr11:18344091-18344102
50	POLR2A	chr11:18343206-18344925	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:203274540..203275064-chr11:18343819..18344505,2	HCT-116	colon:
2	chr11:18343547..18344452-chr11:62608435..62609459,3	Hela-S3	cervix:
3	chr11:18343253..18347316-chr11:18546908..18550670,5	K562	blood:
4	chr11:18340646..18350403-chr11:18414573..18418572,22	K562	blood:
5	chr11:18343277..18345280-chr11:18409232..18413616,5	MCF-7	breast:
6	chr11:18343053..18346262-chr11:18415665..18418898,6	MCF-7	breast:
7	chr11:18341846..18344494-chr11:18547115..18549354,2	MCF-7	breast:
8	chr11:18343610..18344593-chr12:50134989..50135783,2	Hela-S3	cervix:
9	chr11:18342491..18345045-chr11:18415566..18419495,5	MCF-7	breast:
10	chr11:18307340..18310591-chr11:18340181..18344104,5	MCF-7	breast:
11	chr11:18340586..18347042-chr11:18413380..18419628,16	K562	blood:
12	chr11:18317275..18321739-chr11:18342513..18344758,4	K562	blood:
13	chr11:18342562..18345244-chr11:18353891..18356317,3	MCF-7	breast:
14	chr11:18343685..18344556-chr18:657385..658312,2	Hela-S3	cervix:

Variant related genes	Relation type
HPS5	TF binding region
GTF2H1	TF binding region
ENSG00000176912	Chromatin interaction
ENSG00000159388	Chromatin interaction
ENSG00000110768	Chromatin interaction
ENSG00000264603	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000176890	Chromatin interaction
ENSG00000074319	Chromatin interaction
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10741740	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10741743	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766467	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10766469	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10766471	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10832918	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs10832919	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832923	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024606	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024614	0.91[CEU][hapmap]
rs11024622	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12294486	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2037867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2403254	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4150581	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4150589	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150606	0.92[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4150628	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4150644	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4150678	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4757638	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs60889939	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3802967	LDHA	cis	parietal	SCAN
rs3802967	HPS5	cis	cerebellum	SCAN
rs3802967	RPL8	trans	cerebellum	SCAN
rs3802967	PIK3C2A	cis	cerebellum	SCAN
rs3802967	SAA2	cis	cerebellum	SCAN
rs3802967	HPS5	cis	parietal	SCAN
rs3802967	GTF2H1	cis	parietal	SCAN
rs3802967	GTF2H1	cis	Nerve Tibial	GTEx
rs3802967	GTF2H1	cis	cerebellum	SCAN
rs3802967	GTF2H1	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18340000-18345200	Active TSS	GM12878-XiMat	blood
2	chr11:18341000-18346000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:18341400-18345200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr11:18341600-18345200	Active TSS	Psoas Muscle	Psoas
5	chr11:18341600-18345200	Active TSS	HSMMtube	muscle
6	chr11:18341800-18344800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:18341800-18345200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:18342000-18344600	Active TSS	Duodenum Mucosa	Duodenum
9	chr11:18342000-18345200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:18342000-18345400	Active TSS	Aorta	Aorta
11	chr11:18342000-18345600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr11:18342200-18345400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:18342200-18345600	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr11:18342400-18344400	Active TSS	Thymus	Thymus
15	chr11:18342400-18344600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:18342400-18344600	Active TSS	NHEK	skin
17	chr11:18342400-18344800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr11:18342400-18344800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr11:18342400-18344800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:18342400-18344800	Active TSS	HMEC	breast
21	chr11:18342400-18345000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:18342400-18345400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr11:18342400-18345600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:18342400-18345600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:18342400-18346000	Active TSS	K562	blood
26	chr11:18342600-18344400	Active TSS	Placenta	Placenta
27	chr11:18342600-18344800	Active TSS	Fetal Intestine Large	intestine
28	chr11:18342600-18344800	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr11:18342600-18344800	Active TSS	A549	lung
30	chr11:18342600-18344800	Active TSS	HepG2	liver
31	chr11:18342600-18345000	Active TSS	Muscle Satellite Cultured Cells	--
32	chr11:18342600-18345200	Active TSS	Right Atrium	heart
33	chr11:18342600-18345200	Active TSS	NHLF	lung
34	chr11:18342600-18345800	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr11:18342600-18346000	Active TSS	NHDF-Ad	bronchial
36	chr11:18342800-18344400	Active TSS	Primary T cells fromperipheralblood	blood
37	chr11:18342800-18344400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:18342800-18344400	Active TSS	Fetal Thymus	thymus
39	chr11:18342800-18344600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:18342800-18344800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr11:18342800-18344800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:18342800-18344800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:18342800-18344800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr11:18342800-18344800	Active TSS	Fetal Intestine Small	intestine
45	chr11:18342800-18345000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr11:18342800-18345000	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr11:18342800-18345000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:18342800-18345000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:18342800-18345000	Active TSS	Fetal Kidney	kidney
50	chr11:18342800-18345200	Active TSS	H9 Cell Line	embryonic stem cell

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