Variant report

Variant	rs6706375
Chromosome Location	chr2:20249427-20249428
allele	G/T
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	chr2:20249423-20249475	HUVEC	blood vessel:	n/a	n/a
2	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
3	CHD1	chr2:20247605-20252898	IMR90	lung:	n/a	n/a
4	TCF7L2	chr2:20248727-20249495	HEK293	kidney:	n/a	chr2:20249459-20249475 chr2:20249459-20249475
5	HCFC1	chr2:20249219-20253260	Hela-S3	cervix:	n/a	n/a
6	MXI1	chr2:20247504-20253370	SK-N-SH	brain:	n/a	n/a
7	CEBPB	chr2:20249083-20249737	IMR90	lung:	n/a	n/a
8	MAZ	chr2:20249306-20253053	IMR90	lung:	n/a	n/a
9	SPI1	chr2:20249366-20250449	HL-60	blood:	n/a	chr2:20250133-20250146 chr2:20250135-20250142 chr2:20249713-20249726
10	CHD1	chr2:20249058-20249810	H1-hESC	embryonic stem cell:	n/a	n/a
11	NFYB	chr2:20249314-20249510	GM12878	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	chr2:20100261..20103746-chr2:20249026..20255152,7	K562	blood:
5	chr2:20248673..20250285-chr2:20331318..20334095,2	K562	blood:
6	chr2:20236074..20238598-chr2:20248598..20251526,3	K562	blood:
7	chr2:20223805..20226638-chr2:20247959..20250550,2	MCF-7	breast:
8	chr2:20155348..20158077-chr2:20248430..20251683,3	MCF-7	breast:
9	chr2:20249233..20252415-chr2:20424056..20425890,4	MCF-7	breast:

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

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11695154	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1191805	0.85[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]
rs1473887	0.81[AMR][1000 genomes]
rs1473890	0.93[EUR][1000 genomes]
rs1513830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1513831	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16987338	0.94[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34539547	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35030383	0.83[ASN][1000 genomes]
rs36071721	0.92[EUR][1000 genomes]
rs3731673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769759	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769762	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]
rs62109431	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6720508	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558777	0.91[EUR][1000 genomes]
rs7558988	0.89[EUR][1000 genomes]
rs7570360	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7587612	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6706375	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20221400-20249800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:20240600-20249800	Weak transcription	Gastric	stomach
3	chr2:20241400-20249600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:20241600-20250400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:20244000-20249800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:20244000-20250000	Weak transcription	Spleen	Spleen
7	chr2:20247400-20252600	Active TSS	Ovary	ovary
8	chr2:20247600-20249800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:20247600-20250200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:20247800-20249600	Enhancers	Brain Substantia Nigra	brain
11	chr2:20247800-20249600	Enhancers	Stomach Mucosa	stomach
12	chr2:20247800-20249800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:20247800-20250000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:20247800-20250200	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr2:20248000-20249600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr2:20248000-20249600	Flanking Active TSS	HepG2	liver
17	chr2:20248000-20250000	Flanking Active TSS	Osteobl	bone
18	chr2:20248000-20250200	Flanking Active TSS	NHEK	skin
19	chr2:20248000-20250400	Flanking Active TSS	HUVEC	blood vessel
20	chr2:20248000-20250600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr2:20248200-20249600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:20248200-20249600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr2:20248200-20249600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr2:20248200-20249600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr2:20248200-20250200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr2:20248200-20250200	Enhancers	Small Intestine	intestine
27	chr2:20248200-20250600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr2:20248400-20249600	Flanking Active TSS	Brain Angular Gyrus	brain
29	chr2:20248400-20250200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:20248400-20250400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr2:20248400-20250400	Flanking Active TSS	Dnd41	blood
32	chr2:20248400-20252800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:20248400-20252800	Active TSS	Aorta	Aorta
34	chr2:20248600-20251200	Active TSS	Right Atrium	heart
35	chr2:20248600-20252800	Active TSS	Fetal Muscle Leg	muscle
36	chr2:20248600-20252800	Active TSS	Psoas Muscle	Psoas
37	chr2:20248600-20252800	Active TSS	Right Ventricle	heart
38	chr2:20248800-20249600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr2:20248800-20249600	Flanking Active TSS	Fetal Heart	heart
40	chr2:20248800-20249600	Flanking Active TSS	NH-A	brain
41	chr2:20248800-20250000	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr2:20248800-20250200	Flanking Active TSS	Hela-S3	cervix
43	chr2:20248800-20252400	Active TSS	Fetal Intestine Large	intestine
44	chr2:20248800-20252400	Active TSS	Stomach Smooth Muscle	stomach
45	chr2:20248800-20252800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr2:20248800-20252800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:20248800-20252800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:20248800-20253000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:20249000-20249600	Flanking Active TSS	K562	blood
50	chr2:20249000-20249800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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