Variant report

Variant	rs3777442
Chromosome Location	chr6:131209788-131209789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131206831..131209804-chr6:131436324..131438672,3	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12193574	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12526896	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12530288	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs12664445	0.85[ASN][1000 genomes]
rs17180687	0.88[MKK][hapmap]
rs2068147	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2183967	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2275509	0.89[ASN][1000 genomes]
rs3777434	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs3777435	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3777436	0.82[CHB][hapmap]
rs3777440	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777441	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777455	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777458	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3777461	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3777462	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3777465	0.86[ASN][1000 genomes]
rs3777466	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798249	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3798250	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3822861	0.88[ASN][1000 genomes]
rs3822863	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4323333	0.94[ASN][1000 genomes]
rs4357159	0.91[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs4897471	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897472	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4897473	0.86[MKK][hapmap]
rs4897474	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897484	0.86[MKK][hapmap]
rs6569707	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6569708	0.82[CHB][hapmap]
rs6569715	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6908917	0.82[CHD][hapmap]
rs6941712	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs7742376	0.84[CHD][hapmap]
rs7763584	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7773290	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7775013	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs9321257	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9321260	0.86[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs9375779	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9375781	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9375782	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9375783	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375785	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs9375789	0.82[CHD][hapmap]
rs9388861	0.80[CHB][hapmap]
rs9388863	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs9388864	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9388869	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9402292	0.81[JPT][hapmap]
rs9402299	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9483185	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9483192	0.95[ASN][1000 genomes]
rs9492755	0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9492756	0.87[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3777442	VNN3	cis	parietal	SCAN
rs3777442	EPB41L2	cis	parietal	SCAN
rs3777442	ALDH8A1	cis	cerebellum	SCAN
rs3777442	ARG1	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131149400-131213200	Weak transcription	Pancreas	Pancrea
2	chr6:131151600-131216600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:131158200-131214400	Weak transcription	Lung	lung
4	chr6:131159000-131229000	Weak transcription	Colonic Mucosa	Colon
5	chr6:131168800-131214600	Weak transcription	Fetal Kidney	kidney
6	chr6:131170400-131217400	Weak transcription	Psoas Muscle	Psoas
7	chr6:131170600-131213800	Weak transcription	GM12878-XiMat	blood
8	chr6:131171200-131223200	Weak transcription	Right Ventricle	heart
9	chr6:131171400-131220200	Weak transcription	Fetal Brain Male	brain
10	chr6:131175000-131222400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:131175200-131214000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:131175400-131211200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:131175600-131221600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:131179200-131214000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:131179400-131222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:131179600-131210600	Weak transcription	NHEK	skin
17	chr6:131179600-131215000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:131181400-131214400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:131185800-131214400	Weak transcription	Thymus	Thymus
20	chr6:131187000-131214400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:131187000-131223200	Weak transcription	Gastric	stomach
22	chr6:131187200-131216400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:131188200-131216400	Weak transcription	HSMMtube	muscle
24	chr6:131190400-131210600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:131190400-131227000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:131190800-131210800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:131190800-131224200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:131191000-131234400	Weak transcription	Esophagus	oesophagus
29	chr6:131191200-131210600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:131191200-131224200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:131191200-131233000	Weak transcription	Spleen	Spleen
32	chr6:131191400-131211200	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:131191600-131210800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:131191600-131211200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:131191600-131214600	Weak transcription	Fetal Intestine Small	intestine
36	chr6:131194200-131222000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:131195800-131224200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:131198600-131224200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:131198800-131210800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:131201000-131222400	Strong transcription	Dnd41	blood
41	chr6:131201800-131214400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:131201800-131222000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:131203000-131211600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:131203600-131210000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr6:131203600-131234200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:131203800-131210600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:131203800-131210800	Weak transcription	NHDF-Ad	bronchial
48	chr6:131203800-131214400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:131204200-131210800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:131204200-131213200	Weak transcription	Ovary	ovary

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