Variant report

Variant	rs10857650
Chromosome Location	chr10:50030023-50030024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50022212..50024156-chr10:50029662..50031442,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10745284	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10776650	0.80[JPT][hapmap];0.94[ASN][1000 genomes]
rs10776651	0.91[ASN][1000 genomes]
rs10776652	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10857651	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11101517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11101533	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11101558	0.93[JPT][hapmap]
rs17836494	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1904595	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1904600	0.91[ASN][1000 genomes]
rs1904604	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1904605	0.90[ASN][1000 genomes]
rs1913517	0.93[JPT][hapmap]
rs1993985	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2127586	0.91[ASN][1000 genomes]
rs2127592	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2170133	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2377654	1.00[JPT][hapmap]
rs2448541	0.84[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2620878	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2620880	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2620881	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2620882	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2620883	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2620884	0.90[ASN][1000 genomes]
rs2620885	0.90[ASN][1000 genomes]
rs2620887	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2620890	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2620893	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2620894	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2620907	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2663019	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2663020	0.89[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2663021	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2663029	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2663030	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2663033	0.91[ASN][1000 genomes]
rs2663034	0.90[ASN][1000 genomes]
rs2663038	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2663041	1.00[JPT][hapmap]
rs2663049	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2663050	0.91[ASN][1000 genomes]
rs2663052	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2663054	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2663069	0.89[ASN][1000 genomes]
rs2671692	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2671694	0.93[JPT][hapmap]
rs2671710	0.88[ASN][1000 genomes]
rs2671711	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2671712	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2889699	0.91[ASN][1000 genomes]
rs2928404	0.90[ASN][1000 genomes]
rs2940712	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2940728	0.90[ASN][1000 genomes]
rs2940729	0.91[ASN][1000 genomes]
rs2940730	0.87[ASN][1000 genomes]
rs2943245	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2943255	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3747878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3827683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3860191	0.93[JPT][hapmap]
rs4838657	0.88[CEU][hapmap];0.93[JPT][hapmap]
rs6537581	0.94[ASN][1000 genomes]
rs6537582	0.94[ASN][1000 genomes]
rs7068839	1.00[JPT][hapmap]
rs7074067	0.81[ASN][1000 genomes]
rs7078312	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7086333	0.93[JPT][hapmap]
rs7088194	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7094742	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7097397	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7098906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7900483	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7912174	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7913620	0.93[JPT][hapmap]
rs7915025	0.90[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7916558	0.91[ASN][1000 genomes]
rs7922169	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10857650	LOC729156	trans	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50013600-50061000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr10:50015200-50063400	Strong transcription	Primary B cells from cord blood	blood
3	chr10:50016200-50063000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr10:50016200-50063000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr10:50016600-50062400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:50020000-50052000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:50022600-50040400	Weak transcription	Lung	lung
8	chr10:50025000-50062800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr10:50025200-50032000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:50026000-50048200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:50027800-50030200	Enhancers	Fetal Thymus	thymus
12	chr10:50028400-50042000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:50028600-50070200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr10:50028800-50030800	Strong transcription	Spleen	Spleen
15	chr10:50029000-50051400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:50029200-50030200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr10:50029200-50030400	Enhancers	HMEC	breast
18	chr10:50029200-50036600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr10:50029200-50052000	Strong transcription	Primary hematopoietic stem cells	blood
20	chr10:50029400-50032400	Strong transcription	GM12878-XiMat	blood
21	chr10:50029400-50033000	Weak transcription	Liver	Liver
22	chr10:50030000-50035400	Weak transcription	Primary T cells from cord blood	blood

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