Variant report

Variant	rs3856737
Chromosome Location	chr3:42694636-42694637
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	NFIC	chr3:42693953-42695609	SK-N-SH	brain:	n/a	chr3:42694172-42694188 chr3:42694172-42694189
2	POLR2A	chr3:42693885-42695434	U87	brain:	n/a	n/a
3	POLR2A	chr3:42693977-42695668	K562	blood:	n/a	n/a
4	STAT5A	chr3:42694138-42694690	GM12878	blood:	n/a	n/a
5	EP300	chr3:42694012-42695401	ECC-1	luminal epithelium:	n/a	chr3:42694489-42694505 chr3:42694545-42694561
6	POLR2A	chr3:42694106-42694785	SK-N-SH	brain:	n/a	n/a
7	HDAC2	chr3:42694252-42694807	K562	blood:	n/a	n/a
8	JUND	chr3:42692900-42695764	SK-N-SH	brain:	n/a	chr3:42693498-42693510 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693229-42693241 chr3:42693500-42693508 chr3:42693230-42693240 chr3:42693499-42693510
9	POLR2A	chr3:42694026-42695756	HUVEC	blood vessel:	n/a	n/a
10	ELF1	chr3:42693788-42694834	GM12878	blood:	n/a	chr3:42694392-42694403
11	FOSL2	chr3:42692958-42694743	SK-N-SH	brain:	n/a	chr3:42693498-42693510 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693229-42693241 chr3:42693500-42693508 chr3:42693230-42693240 chr3:42693499-42693510
12	MTA3	chr3:42694041-42695061	GM12878	blood:	n/a	n/a
13	TAF1	chr3:42694148-42694702	A549	lung:	n/a	n/a
14	NFIC	chr3:42693913-42695654	ECC-1	luminal epithelium:	n/a	chr3:42694172-42694188 chr3:42694172-42694189
15	RUNX3	chr3:42694165-42694651	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:42694232-42694852	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr3:42693838-42695371	U87	brain:	n/a	n/a
18	SPI1	chr3:42693913-42694737	HL-60	blood:	n/a	chr3:42694392-42694405 chr3:42694394-42694403 chr3:42694252-42694265
19	PML	chr3:42694224-42695009	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:42694250-42695009	K562	blood:	n/a	n/a
21	POLR2A	chr3:42694015-42694985	HCT-116	colon:	n/a	n/a
22	PML	chr3:42694212-42694761	K562	blood:	n/a	n/a
23	NFIC	chr3:42693950-42695598	ECC-1	luminal epithelium:	n/a	chr3:42694172-42694188 chr3:42694172-42694189
24	ZBTB7A	chr3:42694008-42695723	ECC-1	luminal epithelium:	n/a	n/a
25	TAF1	chr3:42694206-42694652	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr3:42694053-42694853	HUVEC	blood vessel:	n/a	n/a
27	TCF12	chr3:42692854-42695443	SK-N-SH	brain:	n/a	chr3:42694507-42694514 chr3:42694856-42694865
28	HCFC1	chr3:42694235-42694666	K562	blood:	n/a	n/a
29	POLR2A	chr3:42694081-42694749	Gliobla	brain:	n/a	n/a
30	POLR2A	chr3:42694272-42694655	IMR90	lung:	n/a	n/a
31	ELF1	chr3:42693956-42694924	HCT-116	colon:	n/a	chr3:42694392-42694403
32	POLR2A	chr3:42694102-42696721	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr3:42693850-42695747	U87	brain:	n/a	n/a
34	POLR2A	chr3:42694255-42694681	GM12878	blood:	n/a	n/a
35	CHD2	chr3:42694245-42694687	Hela-S3	cervix:	n/a	n/a
36	TCF12	chr3:42694130-42697494	ECC-1	luminal epithelium:	n/a	chr3:42694507-42694514 chr3:42697092-42697099 chr3:42694856-42694865
37	MAZ	chr3:42694080-42694816	Hela-S3	cervix:	n/a	n/a
38	FOSL2	chr3:42694102-42694666	A549	lung:	n/a	n/a
39	POLR2A	chr3:42694275-42694738	K562	blood:	n/a	n/a
40	EGR1	chr3:42694218-42694755	K562	blood:	n/a	chr3:42694395-42694404 chr3:42694655-42694668
41	WRNIP1	chr3:42694388-42694776	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:42694041-42694657	GM12878	blood:	n/a	n/a
43	TCF12	chr3:42694019-42694866	A549	lung:	n/a	chr3:42694507-42694514 chr3:42694856-42694865
44	MAZ	chr3:42694148-42694876	K562	blood:	n/a	n/a
45	MAX	chr3:42693977-42694782	K562	blood:	n/a	n/a
46	RCOR1	chr3:42694175-42694956	K562	blood:	n/a	n/a
47	MAZ	chr3:42692512-42697572	IMR90	lung:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42697183-42697193 chr3:42693401-42693411 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
48	MYC	chr3:42694298-42694756	K562	blood:	n/a	n/a
49	HEY1	chr3:42694291-42694674	K562	blood:	n/a	n/a
50	POLR2A	chr3:42694034-42694865	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:
2	chr3:42613871..42615893-chr3:42692209..42694692,2	K562	blood:
3	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
4	chr3:42640678..42643591-chr3:42694568..42696079,2	K562	blood:
5	chr3:42693104..42694831-chr3:42707360..42709210,2	MCF-7	breast:
6	chr3:42640361..42643591-chr3:42693270..42696162,5	K562	blood:
7	chr3:42693324..42695216-chr3:42700072..42702167,2	MCF-7	breast:

Variant related genes	Relation type
ZBTB47	TF binding region
ENSG00000114853	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1062051	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13067987	0.81[EUR][1000 genomes]
rs13072295	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085695	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13089845	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090902	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13093680	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095447	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17074662	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17074664	0.89[ASN][1000 genomes]
rs17074669	0.89[ASN][1000 genomes]
rs17074673	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074674	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074680	0.89[ASN][1000 genomes]
rs17074693	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284303	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284304	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300057	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300058	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302352	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33969824	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33984028	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34683820	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34687113	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34762478	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34801786	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34852409	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34977988	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35216140	0.82[EUR][1000 genomes]
rs35506005	0.82[ASN][1000 genomes]
rs35676838	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35770315	0.89[ASN][1000 genomes]
rs35871059	0.82[EUR][1000 genomes]
rs35890296	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36033201	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043081	0.82[EUR][1000 genomes]
rs3774401	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774402	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774404	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774406	0.82[ASN][1000 genomes]
rs3774407	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846058	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3846059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886782	0.82[ASN][1000 genomes]
rs3900780	0.81[EUR][1000 genomes]
rs56047094	0.82[EUR][1000 genomes]
rs56797870	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57259216	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58868911	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59914338	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60232916	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60348477	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60535002	0.82[EUR][1000 genomes]
rs61149998	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441928	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66786953	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67059259	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67165547	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67533173	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67583158	0.82[EUR][1000 genomes]
rs6771105	0.82[EUR][1000 genomes]
rs6772312	0.81[ASN][1000 genomes]
rs6778982	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782164	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67832425	0.82[EUR][1000 genomes]
rs6788548	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790204	0.81[EUR][1000 genomes]
rs6793186	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795296	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797491	0.82[EUR][1000 genomes]
rs68004576	0.82[EUR][1000 genomes]
rs68028490	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68071013	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72864072	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73829255	0.82[EUR][1000 genomes]
rs7617403	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617736	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7623867	0.81[EUR][1000 genomes]
rs7624628	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42686400-42695000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:42686600-42694800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:42688600-42694800	Weak transcription	Fetal Kidney	kidney
4	chr3:42688800-42694800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:42690600-42694800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:42691600-42694800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr3:42691800-42695200	Weak transcription	Thymus	Thymus
8	chr3:42692000-42694800	Weak transcription	Primary T cells from cord blood	blood
9	chr3:42692200-42694800	Enhancers	Esophagus	oesophagus
10	chr3:42692200-42694800	Enhancers	Placenta	Placenta
11	chr3:42692400-42694800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:42692400-42694800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:42692400-42694800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr3:42692400-42695000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:42692600-42694800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:42692600-42694800	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr3:42692600-42695000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:42692600-42695000	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr3:42692600-42695400	Flanking Active TSS	Osteobl	bone
20	chr3:42692600-42695600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr3:42692600-42695600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr3:42692800-42694800	Enhancers	Lung	lung
23	chr3:42692800-42695000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:42692800-42695000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:42692800-42695000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:42692800-42695000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:42692800-42695000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:42692800-42695200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:42692800-42695200	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr3:42692800-42695200	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr3:42692800-42695400	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr3:42692800-42695400	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr3:42692800-42695400	Flanking Active TSS	HSMMtube	muscle
34	chr3:42693000-42695000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr3:42693000-42695200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:42693000-42695200	Flanking Active TSS	NHDF-Ad	bronchial
37	chr3:42693000-42695400	Flanking Active TSS	HSMM	muscle
38	chr3:42693000-42695600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:42693200-42694800	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr3:42693200-42694800	Enhancers	Spleen	Spleen
41	chr3:42693200-42695200	Enhancers	Fetal Heart	heart
42	chr3:42693200-42695400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
43	chr3:42693200-42695400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:42693200-42695400	Flanking Active TSS	Right Ventricle	heart
45	chr3:42693200-42695400	Flanking Active TSS	A549	lung
46	chr3:42693200-42695400	Flanking Active TSS	Hela-S3	cervix
47	chr3:42693400-42694800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:42693400-42694800	Enhancers	Fetal Intestine Large	intestine
49	chr3:42693400-42695000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:42693400-42695200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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