Variant report

Variant	rs3885634
Chromosome Location	chr10:28357366-28357367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10763644	0.89[CEU][hapmap]
rs10826397	0.84[AMR][1000 genomes]
rs10826398	0.85[MEX][hapmap];0.81[MKK][hapmap];0.86[AMR][1000 genomes]
rs10826402	0.89[CEU][hapmap]
rs11006818	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs11006820	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006823	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006825	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11006826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11006827	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11006830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006832	0.89[CEU][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11006833	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11006834	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11006836	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11006839	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11006840	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11006841	0.82[AMR][1000 genomes]
rs11006843	0.84[AMR][1000 genomes]
rs11006851	0.81[CEU][hapmap]
rs11006852	1.00[CEU][hapmap]
rs11006855	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11006863	0.84[AMR][1000 genomes]
rs11006867	0.84[AMR][1000 genomes]
rs11006869	0.85[MEX][hapmap];0.84[AMR][1000 genomes]
rs11006870	0.81[AMR][1000 genomes]
rs11006873	0.84[AMR][1000 genomes]
rs11006877	0.80[MEX][hapmap];0.84[AMR][1000 genomes]
rs11006880	0.84[AMR][1000 genomes]
rs11006881	0.84[AMR][1000 genomes]
rs11006883	0.82[AMR][1000 genomes]
rs11006884	0.82[AMR][1000 genomes]
rs12220659	0.84[AMR][1000 genomes]
rs12253376	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12415332	0.83[JPT][hapmap]
rs1317790	0.89[CEU][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1574418	1.00[CEU][hapmap]
rs17757844	0.89[CEU][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1892394	0.90[CEU][hapmap]
rs2069202	0.81[CEU][hapmap]
rs2887213	0.85[AMR][1000 genomes]
rs3802519	0.89[CEU][hapmap]
rs3802520	1.00[CEU][hapmap]
rs3802521	0.89[CEU][hapmap]
rs3885635	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4747613	0.84[JPT][hapmap]
rs4749302	0.89[CEU][hapmap]
rs4749306	0.84[JPT][hapmap]
rs56163384	0.86[AMR][1000 genomes]
rs56349465	0.82[AMR][1000 genomes]
rs57764949	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59082756	0.84[AMR][1000 genomes]
rs59246203	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6481499	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6481501	0.84[JPT][hapmap]
rs7071369	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs72801890	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7895285	0.84[AMR][1000 genomes]
rs7903192	0.88[CEU][hapmap]
rs7909706	0.84[JPT][hapmap]
rs7916852	0.89[CEU][hapmap]
rs927676	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv831815	chr10:28235661-28407533	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1052182	chr10:28259142-28361830	Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv831816	chr10:28304698-28493635	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv894988	chr10:28337570-28410989	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv466855	chr10:28341783-28400835	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv550284	chr10:28341783-28400835	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28341200-28377600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr10:28344600-28364400	Weak transcription	Fetal Heart	heart
3	chr10:28346200-28375400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr10:28346600-28364400	Weak transcription	HepG2	liver
5	chr10:28347000-28361200	Weak transcription	Lung	lung
6	chr10:28347000-28363800	Weak transcription	Fetal Stomach	stomach
7	chr10:28347000-28364000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:28347000-28364000	Weak transcription	Pancreas	Pancrea
9	chr10:28347000-28364200	Weak transcription	Esophagus	oesophagus
10	chr10:28347000-28364600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr10:28347000-28375200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:28347000-28380400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr10:28347000-28381000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr10:28347000-28412200	Weak transcription	Left Ventricle	heart
15	chr10:28347000-28414600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr10:28347200-28364000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr10:28347400-28364200	Weak transcription	Fetal Intestine Large	intestine
18	chr10:28347400-28374600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr10:28347400-28377000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr10:28347400-28377200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr10:28347600-28364200	Weak transcription	Primary B cells from cord blood	blood
22	chr10:28348000-28381200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr10:28348200-28357800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:28348200-28364200	Weak transcription	Fetal Intestine Small	intestine
25	chr10:28348200-28365200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr10:28348400-28358800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:28349400-28376600	Weak transcription	Colon Smooth Muscle	Colon
28	chr10:28349600-28364200	Weak transcription	HSMM	muscle
29	chr10:28349800-28358200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr10:28349800-28361800	Weak transcription	Aorta	Aorta
31	chr10:28349800-28364200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:28349800-28364400	Weak transcription	Gastric	stomach
33	chr10:28355400-28358800	Weak transcription	Liver	Liver
34	chr10:28355400-28360400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr10:28355600-28364000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr10:28355800-28360800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr10:28356000-28364000	Weak transcription	HSMMtube	muscle
38	chr10:28356000-28364200	Weak transcription	Adipose Nuclei	Adipose
39	chr10:28356200-28361400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:28356200-28364000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr10:28356200-28364000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr10:28356200-28364400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:28356200-28366200	Weak transcription	Brain Angular Gyrus	brain
44	chr10:28356400-28358400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr10:28356600-28363600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr10:28356600-28364200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr10:28356800-28357800	Weak transcription	Primary T cells from cord blood	blood
48	chr10:28356800-28359600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr10:28356800-28364200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr10:28357000-28358600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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