Variant report

Variant	rs720466
Chromosome Location	chr6:31125705-31125706
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	BRCA1	chr6:31125686-31126511	Hela-S3	cervix:	n/a	n/a
2	MAX	chr6:31125693-31126610	A549	lung:	n/a	n/a
3	POLR2A	chr6:31125634-31126773	U87	brain:	n/a	n/a
4	ZBTB7A	chr6:31125607-31126158	K562	blood:	n/a	chr6:31125721-31125730
5	POLR2A	chr6:31125669-31126501	HCT-116	colon:	n/a	n/a
6	POLR2A	chr6:31125539-31127594	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:31125575-31126195	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr6:31125665-31126576	SK-N-SH	brain:	n/a	n/a
9	SIN3AK20	chr6:31125672-31125994	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr6:31125689-31126035	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr6:31125664-31126621	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr6:31125697-31126172	K562	blood:	n/a	n/a
13	MAZ	chr6:31125452-31126914	IMR90	lung:	n/a	n/a
14	POLR2A	chr6:31125636-31127732	GM12892	blood:	n/a	n/a
15	ZBTB7A	chr6:31125585-31126098	ECC-1	luminal epithelium:	n/a	chr6:31125721-31125730
16	POLR2A	chr6:31125679-31126196	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr6:31125649-31125913	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZBTB7A	chr6:31125660-31126130	HepG2	liver:	n/a	chr6:31125721-31125730
19	POLR2A	chr6:31125649-31126531	HCT-116	colon:	n/a	n/a
20	POLR2A	chr6:31125678-31126628	MCF-7	breast:	n/a	n/a
21	TAF1	chr6:31125614-31126185	K562	blood:	n/a	n/a
22	POLR2A	chr6:31125590-31126790	SK-N-MC	brain:	n/a	n/a
23	MXI1	chr6:31125621-31127412	SK-N-SH	brain:	n/a	n/a
24	ZBTB7A	chr6:31125633-31126043	K562	blood:	n/a	chr6:31125721-31125730
25	POLR2A	chr6:31125671-31126177	HepG2	liver:	n/a	n/a
26	HCFC1	chr6:31125138-31126915	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr6:31125705-31126042	GM12892	blood:	n/a	n/a
28	TAF1	chr6:31125696-31126183	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr6:31125597-31126725	K562	blood:	n/a	n/a
30	NFIC	chr6:31125659-31126586	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:31125640-31126716	U87	brain:	n/a	n/a
32	MAX	chr6:31125653-31126687	K562	blood:	n/a	n/a
33	ZBTB7A	chr6:31125680-31126011	HepG2	liver:	n/a	chr6:31125721-31125730
34	MXI1	chr6:31125636-31127074	IMR90	lung:	n/a	n/a
35	POLR2A	chr6:31125612-31126125	SK-N-MC	brain:	n/a	n/a
36	TAF1	chr6:31125618-31126656	ECC-1	luminal epithelium:	n/a	n/a
37	REST	chr6:31125418-31126716	H1-neurons	neurons:	n/a	chr6:31126223-31126232
38	CEBPD	chr6:31125628-31126572	HepG2	liver:	n/a	n/a
39	SP1	chr6:31125605-31126681	HCT-116	colon:	n/a	chr6:31126258-31126279 chr6:31125998-31126010 chr6:31125973-31125983 chr6:31125906-31125920 chr6:31125973-31125983 chr6:31125998-31126010 chr6:31126278-31126290 chr6:31126280-31126289 chr6:31125999-31126008 chr6:31126278-31126290 chr6:31126062-31126076 chr6:31125907-31125916 chr6:31126279-31126288 chr6:31125896-31125910 chr6:31126204-31126215
40	TAF1	chr6:31125624-31126567	K562	blood:	n/a	n/a
41	POLR2A	chr6:31125655-31128143	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr6:31125618-31126735	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr6:31125673-31126211	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr6:31125695-31126107	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:31125637-31126595	K562	blood:	n/a	n/a
46	ZBTB7A	chr6:31125585-31126425	ECC-1	luminal epithelium:	n/a	chr6:31125721-31125730
47	HDAC2	chr6:31125691-31126725	MCF-7	breast:	n/a	n/a
48	HEY1	chr6:31125610-31126499	HepG2	liver:	n/a	n/a
49	POLR2A	chr6:31125667-31126206	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr6:31125626-31126843	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31124835..31127745-chr6:31135310..31138711,4	MCF-7	breast:
2	chr6:30584033..30586510-chr6:31124123..31126779,2	K562	blood:
3	chr6:31119377..31122828-chr6:31124699..31127188,7	K562	blood:
4	chr20:30192973..30193725-chr6:31125491..31126289,2	HCT-116	colon:
5	chr6:31103871..31105834-chr6:31123155..31127372,3	MCF-7	breast:
6	chr6:31112475..31116177-chr6:31122128..31126125,5	K562	blood:
7	chr6:31120552..31122855-chr6:31123459..31126942,6	MCF-7	breast:

Variant related genes	Relation type
TCF19	TF binding region
CCHCR1	TF binding region
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204531	Chromatin interaction
ENSG00000204540	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000204536	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1062630	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150765	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195316	0.92[ASN][1000 genomes]
rs1265071	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265159	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265177	0.92[ASN][1000 genomes]
rs1265178	0.92[ASN][1000 genomes]
rs130065	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs130076	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs130079	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198298	0.93[ASN][1000 genomes]
rs13204986	0.96[ASN][1000 genomes]
rs13212902	0.84[ASN][1000 genomes]
rs1639110	0.92[ASN][1000 genomes]
rs1793895	0.92[ASN][1000 genomes]
rs28732090	0.92[ASN][1000 genomes]
rs28732092	0.92[ASN][1000 genomes]
rs3094662	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130455	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130457	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130459	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130508	0.92[ASN][1000 genomes]
rs3130510	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720465	0.89[AFR][1000 genomes]
rs887465	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription 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	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
15	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
16	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv884138	chr6:31114573-31129707	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs720466	HLA-B	Cis_1M	lymphoblastoid	RTeQTL
rs720466	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs720466	HCG27	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31124800-31126800	Active TSS	NHLF	lung
2	chr6:31125000-31125800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:31125000-31125800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr6:31125000-31126000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:31125000-31127000	Active TSS	Muscle Satellite Cultured Cells	--
6	chr6:31125000-31127400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:31125000-31127800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:31125200-31125800	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr6:31125200-31125800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:31125200-31125800	Flanking Active TSS	Liver	Liver
11	chr6:31125200-31125800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr6:31125200-31126400	Active TSS	Primary hematopoietic stem cells	blood
13	chr6:31125200-31126800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr6:31125200-31127400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr6:31125200-31127800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:31125400-31125800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr6:31125400-31125800	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr6:31125400-31126200	Active TSS	Stomach Smooth Muscle	stomach
19	chr6:31125400-31126400	Active TSS	Right Ventricle	heart
20	chr6:31125400-31126600	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr6:31125400-31126600	Active TSS	Brain Angular Gyrus	brain
22	chr6:31125400-31126600	Active TSS	Brain Anterior Caudate	brain
23	chr6:31125400-31126600	Active TSS	Brain Cingulate Gyrus	brain
24	chr6:31125400-31126600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr6:31125400-31126600	Active TSS	Duodenum Mucosa	Duodenum
26	chr6:31125400-31126600	Active TSS	Fetal Brain Male	brain
27	chr6:31125400-31126600	Active TSS	Fetal Brain Female	brain
28	chr6:31125400-31126600	Active TSS	Fetal Heart	heart
29	chr6:31125400-31126600	Active TSS	Fetal Intestine Large	intestine
30	chr6:31125400-31126600	Active TSS	Fetal Intestine Small	intestine
31	chr6:31125400-31126600	Active TSS	Fetal Stomach	stomach
32	chr6:31125400-31126600	Active TSS	Stomach Mucosa	stomach
33	chr6:31125400-31126600	Active TSS	HepG2	liver
34	chr6:31125400-31126600	Active TSS	HSMM	muscle
35	chr6:31125400-31126800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:31125400-31126800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:31125400-31126800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:31125400-31126800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:31125400-31126800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:31125400-31126800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:31125400-31126800	Active TSS	Brain Hippocampus Middle	brain
42	chr6:31125400-31126800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:31125400-31126800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr6:31125400-31126800	Active TSS	Fetal Lung	lung
45	chr6:31125400-31126800	Active TSS	Left Ventricle	heart
46	chr6:31125400-31126800	Active TSS	Ovary	ovary
47	chr6:31125400-31126800	Active TSS	Psoas Muscle	Psoas
48	chr6:31125400-31126800	Active TSS	Rectal Smooth Muscle	rectum
49	chr6:31125400-31126800	Active TSS	K562	blood
50	chr6:31125400-31126800	Active TSS	Osteobl	bone

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