Variant report

Variant	rs3769762
Chromosome Location	chr2:20249829-20249830
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	TEAD4	chr2:20249801-20250730	K562	blood:	n/a	n/a
2	MXI1	chr2:20249818-20253177	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:20249742-20250811	GM12878	blood:	n/a	n/a
4	ARID3A	chr2:20249705-20250722	K562	blood:	n/a	n/a
5	REST	chr2:20249044-20253112	H1-neurons	neurons:	n/a	chr2:20250974-20250987 chr2:20251116-20251129 chr2:20251113-20251126 chr2:20252708-20252728 chr2:20251846-20251859 chr2:20251871-20251880
6	SPI1	chr2:20249661-20250599	GM12878	blood:	n/a	chr2:20250133-20250146 chr2:20250135-20250142 chr2:20249713-20249726
7	PML	chr2:20249815-20250711	GM12878	blood:	n/a	n/a
8	EP300	chr2:20249634-20250746	GM12878	blood:	n/a	chr2:20250130-20250144 chr2:20249715-20249724 chr2:20249714-20249728
9	JUN	chr2:20249770-20250219	K562	blood:	n/a	n/a
10	POLR2A	chr2:20249460-20249855	K562	blood:	n/a	n/a
11	STAT3	chr2:20249652-20250549	GM12878	blood:	n/a	n/a
12	GATA1	chr2:20249823-20250808	PBDE	blood:	n/a	chr2:20250794-20250804
13	CHD1	chr2:20247605-20252898	IMR90	lung:	n/a	n/a
14	POLR2A	chr2:20249811-20250800	GM12892	blood:	n/a	n/a
15	FOS	chr2:20249556-20250224	MCF10A-Er-Src	breast:	n/a	chr2:20249717-20249726
16	MYC	chr2:20249767-20249985	MCF10A-Er-Src	breast:	n/a	n/a
17	MAFK	chr2:20249750-20250280	IMR90	lung:	n/a	chr2:20249971-20249981
18	FOS	chr2:20249450-20250372	HUVEC	blood vessel:	n/a	chr2:20249717-20249726
19	ZNF263	chr2:20249503-20252187	HEK293-T-REx	kidney:	n/a	chr2:20250545-20250554
20	POLR2A	chr2:20249628-20252299	K562	blood:	n/a	n/a
21	POLR2A	chr2:20249765-20250492	SK-N-MC	brain:	n/a	n/a
22	CBX3	chr2:20249806-20250828	K562	blood:	n/a	n/a
23	HCFC1	chr2:20249219-20253260	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr2:20249576-20252157	PBDE	blood:	n/a	n/a
25	KAP1	chr2:20249675-20250886	HEK293	kidney:	n/a	n/a
26	FOXM1	chr2:20249753-20250650	GM12878	blood:	n/a	n/a
27	MXI1	chr2:20247504-20253370	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr2:20249749-20252227	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:20249812-20252905	IMR90	lung:	n/a	n/a
30	MXI1	chr2:20249580-20252600	GM12878	blood:	n/a	n/a
31	CTCF	chr2:20249782-20249981	K562	blood:	n/a	n/a
32	MAZ	chr2:20249306-20253053	IMR90	lung:	n/a	n/a
33	ATF1	chr2:20249621-20250736	K562	blood:	n/a	n/a
34	POU2F2	chr2:20249828-20250324	GM12878	blood:	n/a	chr2:20249868-20249880
35	FOS	chr2:20249555-20250142	MCF10A-Er-Src	breast:	n/a	chr2:20249717-20249726
36	TBP	chr2:20249473-20250771	GM12878	blood:	n/a	chr2:20249712-20249723
37	POLR2A	chr2:20249791-20250805	HUVEC	blood vessel:	n/a	n/a
38	KAP1	chr2:20249621-20250334	U2OS	brain:	n/a	n/a
39	MAZ	chr2:20249810-20252166	K562	blood:	n/a	n/a
40	CHD1	chr2:20249433-20250958	GM12878	blood:	n/a	n/a
41	MYC	chr2:20249569-20250191	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr2:20249722-20252906	MCF10A-Er-Src	breast:	n/a	n/a
43	SPI1	chr2:20249366-20250449	HL-60	blood:	n/a	chr2:20250133-20250146 chr2:20250135-20250142 chr2:20249713-20249726
44	MAFF	chr2:20249797-20250729	K562	blood:	n/a	n/a
45	NFIC	chr2:20249709-20250601	GM12878	blood:	n/a	n/a
46	MAZ	chr2:20249779-20252236	GM12878	blood:	n/a	n/a
47	CUX1	chr2:20249577-20250595	K562	blood:	n/a	n/a
48	IRF1	chr2:20249686-20252268	K562	blood:	n/a	chr2:20250687-20250698 chr2:20250131-20250140 chr2:20250687-20250700 chr2:20251848-20251862 chr2:20250688-20250698 chr2:20250684-20250701 chr2:20250688-20250702
49	SIN3A	chr2:20249610-20252383	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr2:20249829-20250668	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20248476..20251356-chr2:20368246..20369984,2	MCF-7	breast:
2	chr2:20208645..20229804-chr2:20247969..20254330,37	MCF-7	breast:
3	chr2:20188631..20191521-chr2:20249258..20251143,2	MCF-7	breast:
4	chr2:20100300..20103104-chr2:20249714..20251596,2	MCF-7	breast:
5	chr2:20100261..20103746-chr2:20249026..20255152,7	K562	blood:
6	chr2:20248673..20250285-chr2:20331318..20334095,2	K562	blood:
7	chr2:20236074..20238598-chr2:20248598..20251526,3	K562	blood:
8	chr2:20249442..20251362-chr2:20288263..20290257,2	K562	blood:
9	chr2:20223805..20226638-chr2:20247959..20250550,2	MCF-7	breast:
10	chr2:20249637..20253449-chr2:20421472..20424385,3	MCF-7	breast:
11	chr2:20155348..20158077-chr2:20248430..20251683,3	MCF-7	breast:
12	chr2:20249233..20252415-chr2:20424056..20425890,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223734	TF binding region
ENSG00000118965	Chromatin interaction
ENSG00000271991	Chromatin interaction
ENSG00000115884	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000227210	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1016316	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11674251	0.87[CEU][hapmap];0.83[ASN][1000 genomes]
rs11689320	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11689431	0.82[CEU][hapmap]
rs11694170	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11695154	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1191805	0.84[EUR][1000 genomes]
rs1191817	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs12988954	0.94[CEU][hapmap];0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs13422363	1.00[YRI][hapmap]
rs1473890	0.92[EUR][1000 genomes]
rs1513830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1513831	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16987338	0.94[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34539547	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35030383	0.83[ASN][1000 genomes]
rs36071721	0.91[EUR][1000 genomes]
rs3731673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769759	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109431	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720508	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558777	0.90[EUR][1000 genomes]
rs7558988	0.88[EUR][1000 genomes]
rs7570360	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7587612	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20241600-20250400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:20244000-20250000	Weak transcription	Spleen	Spleen
3	chr2:20247400-20252600	Active TSS	Ovary	ovary
4	chr2:20247600-20250200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:20247800-20250000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:20247800-20250200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr2:20248000-20250000	Flanking Active TSS	Osteobl	bone
8	chr2:20248000-20250200	Flanking Active TSS	NHEK	skin
9	chr2:20248000-20250400	Flanking Active TSS	HUVEC	blood vessel
10	chr2:20248000-20250600	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr2:20248200-20250200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr2:20248200-20250200	Enhancers	Small Intestine	intestine
13	chr2:20248200-20250600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr2:20248400-20250200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:20248400-20250400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr2:20248400-20250400	Flanking Active TSS	Dnd41	blood
17	chr2:20248400-20252800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:20248400-20252800	Active TSS	Aorta	Aorta
19	chr2:20248600-20251200	Active TSS	Right Atrium	heart
20	chr2:20248600-20252800	Active TSS	Fetal Muscle Leg	muscle
21	chr2:20248600-20252800	Active TSS	Psoas Muscle	Psoas
22	chr2:20248600-20252800	Active TSS	Right Ventricle	heart
23	chr2:20248800-20250000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr2:20248800-20250200	Flanking Active TSS	Hela-S3	cervix
25	chr2:20248800-20252400	Active TSS	Fetal Intestine Large	intestine
26	chr2:20248800-20252400	Active TSS	Stomach Smooth Muscle	stomach
27	chr2:20248800-20252800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:20248800-20252800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:20248800-20252800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:20248800-20253000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:20249000-20250000	Active TSS	Fetal Brain Male	brain
32	chr2:20249000-20250200	Flanking Active TSS	A549	lung
33	chr2:20249000-20250600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr2:20249000-20250800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:20249000-20252200	Active TSS	Fetal Thymus	thymus
36	chr2:20249000-20252200	Active TSS	GM12878-XiMat	blood
37	chr2:20249000-20252400	Active TSS	Colon Smooth Muscle	Colon
38	chr2:20249000-20252400	Active TSS	Fetal Lung	lung
39	chr2:20249000-20252400	Active TSS	HSMM	muscle
40	chr2:20249000-20252600	Active TSS	H9 Cell Line	embryonic stem cell
41	chr2:20249000-20252600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:20249000-20252800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr2:20249000-20252800	Active TSS	H1 Cell Line	embryonic stem cell
44	chr2:20249000-20252800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:20249000-20252800	Active TSS	Fetal Kidney	kidney
46	chr2:20249000-20252800	Active TSS	NHDF-Ad	bronchial
47	chr2:20249000-20252800	Active TSS	NHLF	lung
48	chr2:20249000-20253200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:20249200-20250200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr2:20249200-20250200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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