Variant report

Variant	rs1964092
Chromosome Location	chr2:7153693-7153694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:7147550..7151799-chr2:7153014..7155237,5	MCF-7	breast:
2	chr2:7145702..7149842-chr2:7151104..7154625,5	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11679967	0.86[CEU][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs11689450	0.82[CEU][hapmap]
rs11691419	0.86[CEU][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs13019196	0.82[CEU][hapmap]
rs13030643	0.82[CEU][hapmap]
rs177922	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2460403	0.88[EUR][1000 genomes]
rs2460406	0.87[EUR][1000 genomes]
rs309308	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs309313	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs309315	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs309323	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs367906	0.95[CEU][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs368831	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs369808	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs3755511	0.82[CEU][hapmap]
rs376219	0.90[MEX][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3771993	0.86[EUR][1000 genomes]
rs377617	0.90[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs378548	0.87[EUR][1000 genomes]
rs3821334	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs3821335	0.82[CEU][hapmap]
rs389351	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs389411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs392409	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs392709	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs401164	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs405503	0.87[EUR][1000 genomes]
rs410210	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs412098	0.83[JPT][hapmap]
rs415204	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs416416	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs418312	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs418878	0.87[EUR][1000 genomes]
rs422341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs425247	0.90[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs429349	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs433983	0.82[CEU][hapmap];0.80[MEX][hapmap]
rs434607	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs438627	0.83[JPT][hapmap]
rs447031	0.90[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs447627	0.85[AMR][1000 genomes]
rs449500	0.85[AMR][1000 genomes]
rs451763	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs454999	0.86[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs530431	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1964092	RNF144A	cis	parietal	SCAN
rs1964092	TSSC1	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7101200-7154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr2:7124000-7157600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:7127200-7154000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:7131000-7167600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:7131400-7162400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:7131600-7154200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:7131600-7154200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:7137400-7160200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:7142600-7163000	Weak transcription	Small Intestine	intestine
10	chr2:7144200-7154600	Weak transcription	HepG2	liver
11	chr2:7145200-7156200	Enhancers	Brain Angular Gyrus	brain
12	chr2:7146800-7156000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:7147000-7154800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:7147200-7158600	Enhancers	Colon Smooth Muscle	Colon
15	chr2:7147400-7154000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:7147400-7156000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:7147400-7157000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:7147400-7159200	Weak transcription	Thymus	Thymus
19	chr2:7147600-7155600	Enhancers	NHDF-Ad	bronchial
20	chr2:7148000-7153800	Weak transcription	Fetal Kidney	kidney
21	chr2:7148000-7154000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:7148000-7155800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:7148200-7154000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:7148200-7154000	Weak transcription	Fetal Brain Male	brain
25	chr2:7148200-7156000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr2:7148200-7159400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:7148200-7172600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:7148600-7154400	Weak transcription	Primary B cells from cord blood	blood
29	chr2:7148800-7154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:7148800-7154200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:7148800-7154200	Weak transcription	GM12878-XiMat	blood
32	chr2:7148800-7154600	Weak transcription	Fetal Brain Female	brain
33	chr2:7148800-7155400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:7148800-7156400	Enhancers	Brain Hippocampus Middle	brain
35	chr2:7148800-7158000	Weak transcription	Brain Germinal Matrix	brain
36	chr2:7148800-7159200	Enhancers	Brain Substantia Nigra	brain
37	chr2:7148800-7160200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:7148800-7160800	Enhancers	Fetal Heart	heart
39	chr2:7148800-7171400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:7149000-7157800	Enhancers	Brain Anterior Caudate	brain
41	chr2:7149200-7154000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:7149200-7154400	Weak transcription	K562	blood
43	chr2:7149200-7154600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:7149200-7158200	Weak transcription	Fetal Intestine Small	intestine
45	chr2:7149200-7159200	Enhancers	Brain Cingulate Gyrus	brain
46	chr2:7149200-7159400	Weak transcription	Placenta	Placenta
47	chr2:7149200-7160000	Weak transcription	Esophagus	oesophagus
48	chr2:7149200-7160400	Weak transcription	Lung	lung
49	chr2:7149200-7163800	Weak transcription	Gastric	stomach
50	chr2:7149400-7157000	Weak transcription	Colonic Mucosa	Colon

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