Variant report

Variant	rs2620896
Chromosome Location	chr10:50024030-50024031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50021873..50024313-chr10:50091806..50093411,2	MCF-7	breast:
2	chr10:50022212..50024156-chr10:50029662..50031442,2	MCF-7	breast:
3	chr10:50023366..50027045-chr10:50027536..50030400,3	K562	blood:
4	chr10:50009310..50017840-chr10:50018505..50026491,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128815	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10776647	0.92[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10776648	0.92[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10776649	0.81[EUR][1000 genomes]
rs10857655	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11101511	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101529	0.93[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs11101530	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11101531	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11101532	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1904596	0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2002587	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2002588	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2127590	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2170132	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2250389	0.97[ASN][1000 genomes]
rs2448539	0.93[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs2448540	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2448545	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs2457214	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2620888	0.89[JPT][hapmap]
rs2620889	0.82[JPT][hapmap]
rs2620891	0.92[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2620898	0.93[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2620904	0.93[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2663044	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2663051	0.93[ASN][1000 genomes]
rs2928401	1.00[JPT][hapmap]
rs2940727	0.88[ASN][1000 genomes]
rs2943244	0.89[JPT][hapmap]
rs35932562	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747872	0.88[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747873	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747874	0.92[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs3747875	0.88[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747877	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3860188	0.91[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3860189	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3860190	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537576	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6537580	0.89[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7079766	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7093474	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726786	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7900138	0.88[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap]
rs7913005	0.88[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7919656	0.90[ASN][1000 genomes]
rs877819	0.88[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs877820	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs877821	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831865	chr10:49994254-50164239	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50005200-50026800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:50009600-50028000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:50013600-50028200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr10:50013600-50061000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:50014200-50030000	Weak transcription	Right Atrium	heart
6	chr10:50015200-50063400	Strong transcription	Primary B cells from cord blood	blood
7	chr10:50015600-50029800	Weak transcription	Gastric	stomach
8	chr10:50016200-50063000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr10:50016200-50063000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr10:50016600-50062400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:50019400-50029000	Weak transcription	Primary T cells from cord blood	blood
12	chr10:50020000-50052000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr10:50021200-50027800	Weak transcription	Fetal Thymus	thymus
14	chr10:50022200-50025200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:50022400-50025200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:50022600-50025200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:50022600-50040400	Weak transcription	Lung	lung
18	chr10:50022800-50025200	Weak transcription	Spleen	Spleen
19	chr10:50023000-50025000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:50023200-50025000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr10:50023200-50025000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:50023400-50029200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr10:50023800-50025400	Weak transcription	GM12878-XiMat	blood

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