Variant report

Variant	rs2966809
Chromosome Location	chr5:107550590-107550591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10044509	0.81[CEU][hapmap]
rs10056658	0.90[EUR][1000 genomes]
rs10057274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs10057905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10065182	0.81[CEU][hapmap]
rs10070565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs1019465	0.81[CEU][hapmap]
rs10464048	0.81[CEU][hapmap]
rs10477889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs10477894	0.90[EUR][1000 genomes]
rs10479427	0.81[CEU][hapmap]
rs10900903	0.83[CEU][hapmap]
rs11242663	0.81[CEU][hapmap]
rs12521975	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs13174270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs13174635	0.80[CEU][hapmap]
rs1839224	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044711	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2122157	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs286762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs286765	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs286766	0.93[CHB][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs286768	0.83[EUR][1000 genomes]
rs28868900	0.89[EUR][1000 genomes]
rs2922409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2922410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2922411	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2922413	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2922414	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2922415	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922416	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922419	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2922434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2966794	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2966805	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2966806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2966807	0.91[EUR][1000 genomes]
rs2966808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2966810	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2966811	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2966812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2966815	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2966817	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2966819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34019963	0.90[EUR][1000 genomes]
rs34088844	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35053804	0.92[EUR][1000 genomes]
rs35624833	0.91[EUR][1000 genomes]
rs35959276	0.90[EUR][1000 genomes]
rs3756573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs399438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4276393	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4385196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4957750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66855775	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6860212	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6871109	0.80[CEU][hapmap]
rs6876279	0.83[CEU][hapmap]
rs715638	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534281	chr5:107357579-107674981	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv830441	chr5:107450392-107614557	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv882684	chr5:107521677-107695558	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv830442	chr5:107539150-107697020	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107516200-107584800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:107516800-107551400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:107517000-107571800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr5:107526000-107550800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:107537000-107550600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:107539400-107551000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:107544200-107550600	Weak transcription	Liver	Liver
8	chr5:107546200-107553200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:107546600-107590800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:107547000-107552400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:107547000-107577200	Weak transcription	Fetal Intestine Large	intestine
12	chr5:107548000-107550600	Weak transcription	Primary T cells from cord blood	blood
13	chr5:107548600-107550600	Weak transcription	Primary B cells from cord blood	blood
14	chr5:107548800-107556000	Weak transcription	Left Ventricle	heart
15	chr5:107549000-107552400	Weak transcription	Fetal Heart	heart
16	chr5:107549000-107552400	Weak transcription	NH-A	brain
17	chr5:107549200-107550600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:107549200-107551600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:107549200-107578000	Weak transcription	Pancreas	Pancrea
20	chr5:107549400-107552400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:107549400-107552600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:107549400-107552600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:107549400-107557600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:107549400-107561200	Weak transcription	Fetal Intestine Small	intestine
25	chr5:107550000-107552600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:107550200-107550600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:107550200-107551600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:107550200-107561400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:107550400-107551000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
30	chr5:107550400-107552000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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