Variant report

Variant	rs3104461
Chromosome Location	chr1:77886339-77886340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10518551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162337	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162338	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253226	1.00[JPT][hapmap]
rs12736701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17100530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17379910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17380099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2349965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647485	0.87[YRI][hapmap]
rs2647514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647517	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647521	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2803143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2803146	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2882289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112829	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4342893	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638175	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59417372	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7417056	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1848735	chr1:77885282-77918347	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77872200-77893400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:77872200-77913800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:77876600-77888600	Strong transcription	HSMM	muscle
4	chr1:77878000-77887000	Weak transcription	Brain Angular Gyrus	brain
5	chr1:77878600-77886400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:77878800-77886400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:77879200-77887200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:77879600-77887200	Weak transcription	Fetal Thymus	thymus
9	chr1:77879600-77887800	Weak transcription	Brain Substantia Nigra	brain
10	chr1:77879800-77886600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:77879800-77887200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:77879800-77887400	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:77880000-77887200	Weak transcription	Brain Anterior Caudate	brain
14	chr1:77882600-77889000	Weak transcription	NHLF	lung
15	chr1:77883000-77889800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:77883400-77888600	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr1:77884000-77889400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:77884200-77887000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:77884200-77887200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:77884400-77886800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:77884400-77890400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:77884600-77887200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:77884600-77889600	Weak transcription	Osteobl	bone
24	chr1:77884800-77889400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:77884800-77890600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:77885000-77886800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:77885000-77887200	Weak transcription	HSMMtube	muscle
28	chr1:77885200-77886600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:77885200-77887000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:77885400-77886800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:77885400-77890600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:77885600-77887000	Enhancers	Primary T cells from cord blood	blood
33	chr1:77885600-77887200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:77885600-77888400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:77885600-77888400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr1:77885800-77888200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:77886000-77886400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:77886200-77886600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:77886200-77887200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:77886200-77887400	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:77886200-77887400	Enhancers	Adipose Nuclei	Adipose
42	chr1:77886200-77888000	Strong transcription	NHDF-Ad	bronchial
43	chr1:77886200-77888200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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