Variant report

Variant	rs3761931
Chromosome Location	chr1:114157023-114157024
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	chr1:114156923..114159777-chr1:114160586..114163076,2	K562	blood:
2	chr1:114154767..114157221-chr1:114162340..114164066,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10127930	0.88[EUR][1000 genomes]
rs10489936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1080307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1217384	0.81[EUR][1000 genomes]
rs12723023	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12729708	0.81[EUR][1000 genomes]
rs12730675	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12730735	0.86[EUR][1000 genomes]
rs12731010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12731969	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12734625	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12735104	0.87[EUR][1000 genomes]
rs12739970	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12746609	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12748727	0.87[EUR][1000 genomes]
rs12752932	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12753075	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12753351	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12758546	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12760457	0.87[EUR][1000 genomes]
rs13374352	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17274550	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17274620	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17274634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17359302	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17462614	0.86[EUR][1000 genomes]
rs17508163	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17508814	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17509390	0.87[EUR][1000 genomes]
rs1885454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2040040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2359173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2359174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34042871	0.88[EUR][1000 genomes]
rs34258372	0.91[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34341173	0.87[EUR][1000 genomes]
rs34649199	0.88[EUR][1000 genomes]
rs34698891	0.83[EUR][1000 genomes]
rs34799402	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34857922	0.81[EUR][1000 genomes]
rs34877889	0.86[EUR][1000 genomes]
rs35320278	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35383900	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35836713	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36115604	0.87[EUR][1000 genomes]
rs3747998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3748003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3752953	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs3789595	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789599	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs3789607	0.87[EUR][1000 genomes]
rs3789609	0.86[EUR][1000 genomes]
rs4581284	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55855422	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56257513	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61817579	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61817586	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61817617	0.88[EUR][1000 genomes]
rs61819423	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61819424	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61820162	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6668829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6674848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66782936	0.95[ASN][1000 genomes]
rs6703387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs71662837	0.82[AMR][1000 genomes]
rs7533391	0.81[EUR][1000 genomes]
rs7533605	0.87[EUR][1000 genomes]
rs7549685	0.85[EUR][1000 genomes]
rs7555354	0.87[EUR][1000 genomes]
rs9803891	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012324	chr1:114135133-114206843	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3761931	CD58	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114100600-114173400	Weak transcription	Gastric	stomach
2	chr1:114119200-114172400	Weak transcription	Pancreas	Pancrea
3	chr1:114119200-114173000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:114124400-114172400	Weak transcription	Aorta	Aorta
5	chr1:114126600-114157200	Weak transcription	HUVEC	blood vessel
6	chr1:114134600-114166400	Weak transcription	Hela-S3	cervix
7	chr1:114136800-114158800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:114139800-114157400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:114139800-114160000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:114140000-114157400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:114140400-114157800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:114140600-114162200	Weak transcription	NHDF-Ad	bronchial
13	chr1:114140600-114172800	Weak transcription	Colonic Mucosa	Colon
14	chr1:114140800-114162600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:114141000-114157800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:114141000-114162600	Weak transcription	Fetal Intestine Large	intestine
17	chr1:114141200-114162200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:114141400-114162400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:114145600-114157600	Weak transcription	Fetal Brain Female	brain
20	chr1:114145600-114160800	Weak transcription	Fetal Intestine Small	intestine
21	chr1:114146200-114163200	Weak transcription	Fetal Lung	lung
22	chr1:114147200-114163400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:114151400-114157200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:114151400-114157400	Weak transcription	Brain Germinal Matrix	brain
25	chr1:114151400-114172600	Weak transcription	Ovary	ovary
26	chr1:114151800-114166400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:114153000-114163600	Weak transcription	Fetal Kidney	kidney
28	chr1:114153600-114168400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:114154000-114172400	Weak transcription	Fetal Stomach	stomach
30	chr1:114155400-114162000	Weak transcription	Liver	Liver
31	chr1:114156200-114170000	Weak transcription	Small Intestine	intestine
32	chr1:114156600-114157400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:114156600-114158600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:114156600-114158600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:114156800-114157200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:114156800-114158400	Enhancers	Fetal Heart	heart
37	chr1:114157000-114157400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:114157000-114157600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:114157000-114157600	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr1:114157000-114158000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:114157000-114158000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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