Variant report

Variant	rs3777589
Chromosome Location	chr6:45920934-45920935
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	chr6:45919715..45922197-chr6:45926352..45928552,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001938	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757345	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204333	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1204334	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1204335	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12192179	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12198337	0.86[ASN][1000 genomes]
rs12211807	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12662995	0.88[AFR][1000 genomes]
rs1308732	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1890368	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]
rs1890369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1999908	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396580	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734206	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777565	0.83[MEX][hapmap]
rs3777575	0.88[AFR][1000 genomes]
rs3777582	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs3777583	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777587	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777590	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]
rs3777591	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777592	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236087	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4429946	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4563714	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711836	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6909306	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922752	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73460651	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs949678	0.86[ASW][hapmap];0.88[AFR][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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3777589	GPR111	cis	parietal	SCAN
rs3777589	CDC5L	cis	cerebellum	SCAN
rs3777589	SUPT3H	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45911000-45923600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:45912600-45923000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
3	chr6:45912800-45928400	Weak transcription	Spleen	Spleen
4	chr6:45917200-45924800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:45918800-45938400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:45919000-45921200	Enhancers	Fetal Heart	heart
7	chr6:45919000-45921400	Enhancers	Psoas Muscle	Psoas
8	chr6:45919000-45921400	Enhancers	Right Atrium	heart
9	chr6:45919000-45921400	Enhancers	HSMMtube	muscle
10	chr6:45919000-45921600	Genic enhancers	Left Ventricle	heart
11	chr6:45919200-45921400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:45919200-45921600	Genic enhancers	Right Ventricle	heart
13	chr6:45919200-45923000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
14	chr6:45919200-45923200	Genic enhancers	Rectal Mucosa Donor 31	rectum
15	chr6:45919400-45921400	Strong transcription	Fetal Intestine Small	intestine
16	chr6:45919400-45923200	Strong transcription	Fetal Intestine Large	intestine
17	chr6:45919600-45923800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:45919600-45928000	Weak transcription	Adipose Nuclei	Adipose
19	chr6:45920000-45921000	Enhancers	Fetal Kidney	kidney
20	chr6:45920000-45921800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr6:45920000-45922800	Weak transcription	Pancreas	Pancrea
22	chr6:45920000-45927200	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:45920000-45927200	Weak transcription	Placenta	Placenta
24	chr6:45920000-45928200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:45920000-45934800	Weak transcription	Colonic Mucosa	Colon
26	chr6:45920200-45926600	Weak transcription	Fetal Lung	lung
27	chr6:45920600-45922200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:45920800-45921000	Weak transcription	Lung	lung
29	chr6:45920800-45924400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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