Variant report

Variant	rs6781143
Chromosome Location	chr3:19989229-19989230
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	POLR2A	chr3:19988773-19989680	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:19987362-19989595	K562	blood:	n/a	n/a
3	HCFC1	chr3:19987605-19989689	K562	blood:	n/a	n/a
4	RUNX3	chr3:19987795-19989519	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:19987558-19989602	GM18951	blood:	n/a	n/a
6	POLR2A	chr3:19986887-19989909	GM12891	blood:	n/a	n/a
7	STAT1	chr3:19987955-19989668	GM12878	blood:	n/a	chr3:19988530-19988542 chr3:19989252-19989264 chr3:19989188-19989197 chr3:19988321-19988329 chr3:19989110-19989122
8	TAF7	chr3:19988783-19989370	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOS	chr3:19989068-19989592	MCF10A-Er-Src	breast:	n/a	chr3:19989188-19989197 chr3:19989189-19989198 chr3:19989190-19989201 chr3:19989187-19989199 chr3:19989188-19989198 chr3:19989187-19989198
10	SIN3AK20	chr3:19987338-19989938	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:19988297-19989442	ECC-1	luminal epithelium:	n/a	n/a
12	EP300	chr3:19988051-19989533	GM12878	blood:	n/a	chr3:19989189-19989198 chr3:19988330-19988346 chr3:19988621-19988637
13	CTCF	chr3:19989140-19989290	HCPEpiC	choroid plexus:	n/a	chr3:19989265-19989286 chr3:19989198-19989207
14	HEY1	chr3:19987858-19989594	K562	blood:	n/a	n/a
15	ZBTB7A	chr3:19988646-19989469	ECC-1	luminal epithelium:	n/a	n/a
16	CREB1	chr3:19988089-19989745	HepG2	liver:	n/a	n/a
17	RAD21	chr3:19988973-19989393	SK-N-SH_RA	brain:	n/a	chr3:19989040-19989053 chr3:19989269-19989281
18	POLR2A	chr3:19988117-19989553	MCF-7	breast:	n/a	n/a
19	MAX	chr3:19987921-19989653	HepG2	liver:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
20	POU2F2	chr3:19989094-19989471	GM12891	blood:	n/a	n/a
21	SMARCC1	chr3:19986964-19989766	Hela-S3	cervix:	n/a	chr3:19989188-19989197 chr3:19989189-19989198
22	SIN3AK20	chr3:19988033-19989755	K562	blood:	n/a	n/a
23	POLR2A	chr3:19987474-19989718	GM12878	blood:	n/a	n/a
24	MAX	chr3:19988142-19989678	MCF-7	breast:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
25	MYC	chr3:19988199-19989610	MCF10A-Er-Src	breast:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
26	CUX1	chr3:19989021-19990564	K562	blood:	n/a	n/a
27	POLR2A	chr3:19987476-19989652	U87	brain:	n/a	n/a
28	POLR2A	chr3:19987594-19989784	GM18505	blood:	n/a	n/a
29	HMGN3	chr3:19987829-19989561	K562	blood:	n/a	chr3:19989190-19989199
30	HEY1	chr3:19989172-19989595	HepG2	liver:	n/a	n/a
31	YY1	chr3:19988002-19989624	NT2-D1	testis:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19988151-19988159 chr3:19989258-19989280
32	FOSL1	chr3:19988939-19989332	K562	blood:	n/a	chr3:19989188-19989197 chr3:19989189-19989198 chr3:19989190-19989201 chr3:19989187-19989199 chr3:19989188-19989198
33	GABPA	chr3:19988130-19989410	SK-N-SH	brain:	n/a	chr3:19988538-19988545
34	POLR2A	chr3:19987565-19989776	MCF-7	breast:	n/a	n/a
35	POLR2A	chr3:19987429-19989814	H1-hESC	embryonic stem cell:	n/a	n/a
36	BHLHE40	chr3:19987806-19989437	GM12878	blood:	n/a	chr3:19988614-19988630
37	TBP	chr3:19986938-19989974	K562	blood:	n/a	n/a
38	YY1	chr3:19987910-19989745	K562	blood:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19987999-19988008 chr3:19988151-19988159 chr3:19989258-19989280
39	TAF1	chr3:19987973-19989612	H1-neurons	neurons:	n/a	n/a
40	CHD2	chr3:19987637-19989399	H1-hESC	embryonic stem cell:	n/a	chr3:19989363-19989373
41	WRNIP1	chr3:19987590-19989775	GM12878	blood:	n/a	n/a
42	RFX5	chr3:19989163-19989402	HepG2	liver:	n/a	n/a
43	POLR2A	chr3:19987007-19989845	K562	blood:	n/a	n/a
44	YY1	chr3:19988848-19989527	GM12891	blood:	n/a	chr3:19989269-19989277 chr3:19989258-19989280
45	MYC	chr3:19989153-19989460	MCF-7	breast:	n/a	chr3:19989189-19989198
46	E2F4	chr3:19987975-19989588	K562	blood:	n/a	chr3:19988690-19988700 chr3:19987999-19988008 chr3:19988611-19988620 chr3:19987996-19988008 chr3:19988615-19988625
47	POLR2A	chr3:19986884-19989655	Hela-S3	cervix:	n/a	n/a
48	MAFK	chr3:19988897-19990057	Hela-S3	cervix:	n/a	chr3:19989882-19989896 chr3:19989888-19989899 chr3:19989881-19989897 chr3:19989884-19989899 chr3:19989879-19989899
49	CTCF	chr3:19989206-19989310	MCF-7	breast:	n/a	chr3:19989265-19989286
50	YY1	chr3:19987942-19989572	K562	blood:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19987999-19988008 chr3:19988151-19988159 chr3:19989258-19989280

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:19989218-19989268	SAEC	small airway:	n/a
2	chr3:19989218-19989268	Hela-S3	cervix:	n/a
3	chr3:19989218-19989268	A549	lung:	n/a
4	chr3:19989218-19989268	HCT-116	colon:	n/a
5	chr3:19989218-19989268	T-47D	breast:	n/a
6	chr3:19989218-19989268	U87	brain:	n/a
7	chr3:19989218-19989268	HRE	kidney:	n/a
8	chr3:19989218-19989268	NH-A	brain:	n/a
9	chr3:19989218-19989268	AG10803	skin:	n/a
10	chr3:19989218-19989268	HCM	heart:	n/a
11	chr3:19989218-19989268	AG09319	gingival:	n/a
12	chr3:19989218-19989268	GM06990	blood:	n/a
13	chr3:19989218-19989268	Jurkat	blood:	n/a
14	chr3:19989218-19989268	PrEC	prostate:	n/a
15	chr3:19989218-19989268	ovcar-3	ovarian:	n/a
16	chr3:19989218-19989268	PANC-1	pancreas:	n/a
17	chr3:19989218-19989268	HIPEpiC	eye:	n/a
18	chr3:19989218-19989268	HPAEpiC	pulmonary alveolar:	n/a
19	chr3:19989218-19989268	K562	blood:	n/a
20	chr3:19989218-19989268	HRPEpiC	eye:	n/a
21	chr3:19989218-19989268	AG04449	skin:	fetal
22	chr3:19989218-19989268	AG09309	skin:	n/a
23	chr3:19989218-19989268	RPTEC	kidney:	n/a
24	chr3:19989218-19989268	HL-60	blood:	n/a
25	chr3:19989218-19989268	H1-hESC	embryonic stem cell:	embryo
26	chr3:19989218-19989268	GM12892	blood:	n/a
27	chr3:19989218-19989268	NHDF-neo	bronchial:	n/a
28	chr3:19989218-19989268	MCF10A-Er-Src	breast:	n/a
29	chr3:19989218-19989268	AG04450	lung:	fetal
30	chr3:19989218-19989268	GM12891	blood:	n/a
31	chr3:19989218-19989268	MCF-7	breast:	n/a
32	chr3:19989218-19989268	SK-N-SH	brain:	n/a
33	chr3:19989218-19989268	SK-N-SH_RA	brain:	n/a
34	chr3:19989218-19989268	CMK	blood:	n/a
35	chr3:19989218-19989268	HNPCEpiC	eye:	n/a
36	chr3:19989218-19989268	HEK293	kidney:	embryo
37	chr3:19989218-19989268	ProgFib	skin:	n/a
38	chr3:19989218-19989268	HepG2	liver:	n/a
39	chr3:19989218-19989268	BE2_C	brain:	n/a
40	chr3:19989218-19989268	Caco-2	colon:	n/a
41	chr3:19989218-19989268	HEEpiC	esophagus:	n/a
42	chr3:19989218-19989268	HUVEC	blood vessel:	n/a
43	chr3:19989218-19989268	HRCEpiC	kidney:	n/a
44	chr3:19989218-19989268	IMR90	lung:	fetal
45	chr3:19989218-19989268	HCPEpiC	choroid plexus:	n/a
46	chr3:19989218-19989268	NHBE	bronchial:	n/a
47	chr3:19989218-19989268	PFSK-1	brain:	n/a
48	chr3:19989218-19989268	AoSMC	blood vessel:	n/a
49	chr3:19989218-19989268	SK-N-MC	brain:	n/a
50	chr3:19989218-19989268	Hepatocyte	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987782..19990680-chr3:20013275..20017779,4	K562	blood:
3	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
4	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
5	chr3:19987513..19990087-chr3:20080861..20083140,3	MCF-7	breast:
6	chr3:19985145..19990136-chr3:20225418..20228312,6	K562	blood:
7	chr3:19975611..19979082-chr3:19987774..19990681,3	MCF-7	breast:
8	chr3:19188168..19190474-chr3:19988134..19989911,2	MCF-7	breast:
9	chr14:24899081..24899637-chr3:19988552..19989514,2	Hela-S3	cervix:
10	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:
11	chr17:33895021..33895646-chr3:19988844..19989353,2	Hela-S3	cervix:

Variant related genes	Relation type
HSPA8P18	TF binding region
RAB5A	TF binding region
EFHB	TF binding region
HSPA8P18	CpG island
RAB5A	CpG island
EFHB	CpG island
ENSG00000183960	Chromatin interaction
ENSG00000163576	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000267321	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000100441	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12486406	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12489907	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12496392	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13078869	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13079277	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13098054	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2170342	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2686325	0.85[CEU][hapmap]
rs34050713	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34468236	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34955379	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35094497	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35757621	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4302401	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6778866	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7625149	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8682	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19986800-19990200	Active TSS	Duodenum Mucosa	Duodenum
2	chr3:19987000-19989600	Active TSS	Liver	Liver
3	chr3:19987200-19989800	Active TSS	Pancreas	Pancrea
4	chr3:19987200-19990400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:19987200-19990400	Active TSS	Placenta	Placenta
6	chr3:19987200-19990600	Active TSS	K562	blood
7	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:19987400-19989400	Active TSS	Brain Anterior Caudate	brain
9	chr3:19987400-19989400	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:19987400-19989400	Active TSS	Rectal Smooth Muscle	rectum
11	chr3:19987400-19989800	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr3:19987400-19990000	Active TSS	Brain Germinal Matrix	brain
13	chr3:19987400-19990000	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr3:19987400-19990000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr3:19987400-19990000	Active TSS	A549	lung
16	chr3:19987400-19990200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:19987400-19990200	Active TSS	HSMM	muscle
18	chr3:19987400-19990400	Active TSS	NHDF-Ad	bronchial
19	chr3:19987400-19990800	Active TSS	Right Atrium	heart
20	chr3:19987400-19990800	Active TSS	HSMMtube	muscle
21	chr3:19987400-19991400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:19987600-19989400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:19987600-19989400	Active TSS	Fetal Brain Female	brain
24	chr3:19987600-19989600	Active TSS	Brain Cingulate Gyrus	brain
25	chr3:19987600-19989800	Active TSS	Brain Hippocampus Middle	brain
26	chr3:19987600-19989800	Active TSS	Left Ventricle	heart
27	chr3:19987600-19989800	Active TSS	Lung	lung
28	chr3:19987600-19990000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:19987600-19990000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:19987600-19990000	Active TSS	Ovary	ovary
31	chr3:19987600-19990000	Active TSS	Thymus	Thymus
32	chr3:19987600-19990200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:19987600-19990200	Active TSS	Colon Smooth Muscle	Colon
34	chr3:19987600-19990400	Active TSS	Colonic Mucosa	Colon
35	chr3:19987600-19990400	Active TSS	Fetal Kidney	kidney
36	chr3:19987600-19990800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr3:19987600-19991000	Active TSS	NHLF	lung
38	chr3:19987600-19991600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:19987800-19989800	Active TSS	Esophagus	oesophagus
40	chr3:19987800-19989800	Active TSS	Fetal Heart	heart
41	chr3:19987800-19989800	Active TSS	Small Intestine	intestine
42	chr3:19987800-19990000	Active TSS	Aorta	Aorta
43	chr3:19987800-19990000	Active TSS	Fetal Muscle Trunk	muscle
44	chr3:19987800-19990000	Active TSS	Stomach Mucosa	stomach
45	chr3:19987800-19990400	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr3:19987800-19990400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:19987800-19990800	Active TSS	Psoas Muscle	Psoas
48	chr3:19987800-19990800	Active TSS	Right Ventricle	heart
49	chr3:19987800-19991400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr3:19987800-19991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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