Variant report

Variant	rs2245189
Chromosome Location	chr1:77946687-77946688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11800652	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11810135	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12564592	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12564604	0.82[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12566093	0.84[ASN][1000 genomes]
rs12568374	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12568376	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12569104	1.00[CEU][hapmap]
rs17100791	1.00[CEU][hapmap]
rs17100850	1.00[CEU][hapmap]
rs2270539	1.00[CEU][hapmap]
rs2291689	1.00[CEU][hapmap]
rs2291690	1.00[CEU][hapmap]
rs2647496	0.87[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4949655	1.00[JPT][hapmap]
rs55848622	0.84[ASN][1000 genomes]
rs56910202	0.84[ASN][1000 genomes]
rs57744162	0.84[ASN][1000 genomes]
rs57754896	0.84[ASN][1000 genomes]
rs57940344	0.84[ASN][1000 genomes]
rs58143971	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58397190	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58958142	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59029032	0.84[ASN][1000 genomes]
rs59043705	0.84[ASN][1000 genomes]
rs59076612	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59361407	0.84[ASN][1000 genomes]
rs59623467	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59913458	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60207382	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60645967	0.84[ASN][1000 genomes]
rs61080952	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61553470	0.84[ASN][1000 genomes]
rs61575581	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6664497	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6680677	0.87[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs74090603	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74090608	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74090614	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74090617	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74090618	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74090619	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74092623	0.84[ASN][1000 genomes]
rs74092624	0.84[ASN][1000 genomes]
rs74092625	0.84[ASN][1000 genomes]
rs74092627	0.84[ASN][1000 genomes]
rs74092641	0.84[ASN][1000 genomes]
rs74092642	0.84[ASN][1000 genomes]
rs74092644	0.84[ASN][1000 genomes]
rs74092645	0.84[ASN][1000 genomes]
rs74092649	0.84[ASN][1000 genomes]
rs74092650	0.84[ASN][1000 genomes]
rs74092651	0.84[ASN][1000 genomes]
rs74092654	0.84[ASN][1000 genomes]
rs74092655	0.84[ASN][1000 genomes]
rs74092659	0.84[ASN][1000 genomes]
rs74092660	0.84[ASN][1000 genomes]
rs74092662	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7524107	0.84[ASN][1000 genomes]
rs7532905	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv462095	chr1:77903611-77951460	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv546592	chr1:77903611-77951460	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77913200-77968400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:77914600-77955600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:77934200-77948800	Weak transcription	Right Atrium	heart
4	chr1:77934600-77955200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:77935600-77955800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:77935800-77954800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:77938200-77948800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:77940200-77955800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:77940400-77946800	Weak transcription	Brain Substantia Nigra	brain
10	chr1:77940400-77954800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:77940400-77955400	Weak transcription	NHLF	lung
12	chr1:77940600-77954800	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:77940600-77955600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:77940600-77960800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:77940800-77955400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:77943600-77947000	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr1:77944800-77955400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:77945400-77958600	Weak transcription	Primary T cells from cord blood	blood
19	chr1:77945800-77961600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:77946200-77951800	Weak transcription	HSMM	muscle
21	chr1:77946400-77947000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:77946400-77947000	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr1:77946400-77950000	Weak transcription	NHDF-Ad	bronchial

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