Variant report

Variant	rs3769760
Chromosome Location	chr2:20248159-20248160
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	CHD1	chr2:20247605-20252898	IMR90	lung:	n/a	n/a
2	STAT3	chr2:20247945-20248203	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr2:20247504-20253370	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20208645..20229804-chr2:20247969..20254330,37	MCF-7	breast:
2	chr2:20246745..20249019-chr2:20548849..20550388,2	MCF-7	breast:
3	chr2:20223805..20226638-chr2:20247959..20250550,2	MCF-7	breast:
4	chr2:20243160..20246109-chr2:20246463..20248277,2	K562	blood:

Variant related genes	Relation type
ENSG00000223734	TF binding region
ENSG00000055917	Chromatin interaction
ENSG00000132031	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1016316	1.00[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11674251	0.87[CEU][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs11689320	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11689431	0.82[CEU][hapmap];0.84[CHD][hapmap]
rs11694170	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11695154	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1191805	0.85[EUR][1000 genomes]
rs1191817	0.85[EUR][1000 genomes]
rs12988954	0.94[CEU][hapmap];0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs1473890	0.93[EUR][1000 genomes]
rs1513830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1513831	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16987338	0.94[CEU][hapmap];0.83[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];0.92[CHD][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[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];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769759	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];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109431	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706375	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]
rs6720508	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558777	0.91[EUR][1000 genomes]
rs7558988	0.89[EUR][1000 genomes]
rs7570360	0.93[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
rs3769760	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 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	chr2:20234800-20248200	Weak transcription	Psoas Muscle	Psoas
3	chr2:20237800-20249000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:20238000-20248200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:20238600-20248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:20240600-20248200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:20240600-20248200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:20240600-20248200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:20240600-20248200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:20240600-20248200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:20240600-20249200	Weak transcription	Colonic Mucosa	Colon
12	chr2:20240600-20249800	Weak transcription	Gastric	stomach
13	chr2:20240800-20248200	Weak transcription	Brain Germinal Matrix	brain
14	chr2:20240800-20248400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:20240800-20248400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:20240800-20248400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:20240800-20248400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:20240800-20249000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:20240800-20249400	Weak transcription	Placenta	Placenta
20	chr2:20241000-20249000	Weak transcription	Fetal Thymus	thymus
21	chr2:20241400-20248200	Weak transcription	Dnd41	blood
22	chr2:20241400-20248600	Weak transcription	Thymus	Thymus
23	chr2:20241400-20249600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:20241600-20248800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:20241600-20250400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:20242200-20249400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:20242600-20248200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:20242600-20248400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:20244000-20248200	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:20244000-20248200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:20244000-20249400	Weak transcription	Pancreas	Pancrea
32	chr2:20244000-20249800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:20244000-20250000	Weak transcription	Spleen	Spleen
34	chr2:20244200-20248200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:20244200-20248200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:20244200-20248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:20244200-20248200	Weak transcription	Primary T cells from cord blood	blood
38	chr2:20244200-20248400	Weak transcription	Brain Anterior Caudate	brain
39	chr2:20244200-20248400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:20244800-20248200	Weak transcription	Brain Angular Gyrus	brain
41	chr2:20245200-20248200	Weak transcription	Right Atrium	heart
42	chr2:20245200-20248200	Weak transcription	Right Ventricle	heart
43	chr2:20245200-20248200	Weak transcription	Small Intestine	intestine
44	chr2:20246400-20248200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:20246800-20249400	Weak transcription	Left Ventricle	heart
46	chr2:20247000-20249200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:20247000-20249400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:20247000-20249400	Weak transcription	Lung	lung
49	chr2:20247400-20248200	Enhancers	Fetal Brain Male	brain
50	chr2:20247400-20248400	Enhancers	Primary T helper cells PMA-I stimulated	--

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