Variant report

Variant	rs13096371
Chromosome Location	chr3:46247096-46247097
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46234025..46236211-chr3:46246101..46248526,2	MCF-7	breast:
2	chr3:46242531..46244471-chr3:46245460..46247325,2	K562	blood:
3	chr3:46247078..46249229-chr3:46254602..46257153,3	MCF-7	breast:

Extended variants
information (count: 155 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs10510748	0.89[EUR][1000 genomes]
rs10510749	0.92[EUR][1000 genomes]
rs10510750	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs11919943	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11926063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11929489	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059906	0.92[EUR][1000 genomes]
rs13060713	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13060802	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13061548	0.92[EUR][1000 genomes]
rs13062450	0.92[EUR][1000 genomes]
rs13062523	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13069467	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13069750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13069845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13070099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073976	1.00[CEU][hapmap]
rs13075270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075836	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13080979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13082995	0.92[EUR][1000 genomes]
rs13083881	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13083914	0.92[EUR][1000 genomes]
rs13084057	0.90[EUR][1000 genomes]
rs13084175	0.90[EUR][1000 genomes]
rs13088766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089907	0.92[EUR][1000 genomes]
rs13090848	0.89[EUR][1000 genomes]
rs13092160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096325	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13096808	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs13096873	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13096905	1.00[AFR][1000 genomes]
rs13097340	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13097666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13098911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13100243	1.00[CEU][hapmap]
rs1542755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17216717	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17217831	1.00[CEU][hapmap]
rs17282797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17282922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17283712	1.00[CEU][hapmap]
rs2131092	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2373156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2856762	0.87[CEU][hapmap]
rs3091310	1.00[CEU][hapmap]
rs3091314	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3136667	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs3136672	0.92[EUR][1000 genomes]
rs3136673	0.92[EUR][1000 genomes]
rs3176824	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33998492	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34005848	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34013035	0.92[EUR][1000 genomes]
rs34047458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34059564	0.92[EUR][1000 genomes]
rs34101673	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34134191	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34194160	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34198655	0.92[EUR][1000 genomes]
rs34280313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34289272	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34340501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34376347	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34378541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34401473	0.90[EUR][1000 genomes]
rs34406035	1.00[AFR][1000 genomes]
rs34409248	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34414382	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34423195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34498313	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523728	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34531115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34558763	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34567015	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34570200	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34611049	0.92[EUR][1000 genomes]
rs34625088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34677490	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34692251	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34693386	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34745455	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34759782	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34865316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34870159	0.90[EUR][1000 genomes]
rs34897745	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34919616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34920132	0.91[EUR][1000 genomes]
rs34985947	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34996127	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35111399	0.96[EUR][1000 genomes]
rs35178150	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35195804	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35288652	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35335084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35354367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35429781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35431271	1.00[ASN][1000 genomes]
rs35434266	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35481399	1.00[ASN][1000 genomes]
rs35560301	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35566550	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35587265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35613615	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35614049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35617677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35678191	1.00[ASN][1000 genomes]
rs35685805	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35754688	0.90[EUR][1000 genomes]
rs35775079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35853141	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35919278	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35942803	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35960950	0.89[EUR][1000 genomes]
rs35984988	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36000011	1.00[ASN][1000 genomes]
rs36010446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36048333	1.00[AFR][1000 genomes]
rs36189995	0.90[EUR][1000 genomes]
rs3774630	0.93[EUR][1000 genomes]
rs41432345	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41537946	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987053	1.00[CEU][hapmap]
rs57115330	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6765904	0.92[EUR][1000 genomes]
rs6775046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71327035	0.89[EUR][1000 genomes]
rs71327036	0.89[EUR][1000 genomes]
rs71327038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71327039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71327040	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71327041	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71327042	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs71327043	1.00[ASN][1000 genomes]
rs71327044	1.00[ASN][1000 genomes]
rs71615441	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7620586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7624155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7628489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7631551	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs7651539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9832730	1.00[CEU][hapmap]
rs9838191	1.00[CEU][hapmap]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13096371	CCR1	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46235400-46247600	Weak transcription	Placenta	Placenta
2	chr3:46235400-46249600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:46239800-46249400	Weak transcription	Primary T cells from cord blood	blood
4	chr3:46241600-46247400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:46242800-46247400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
6	chr3:46243000-46249000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:46243400-46247800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:46243600-46247200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:46243800-46249400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:46245200-46248800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:46245400-46248000	Weak transcription	Lung	lung
12	chr3:46245600-46247600	Weak transcription	Fetal Lung	lung
13	chr3:46245600-46248000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:46245600-46251800	Weak transcription	Spleen	Spleen
15	chr3:46245800-46248200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:46246200-46247200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
17	chr3:46246200-46248200	Enhancers	Fetal Thymus	thymus
18	chr3:46246400-46247800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:46246400-46248000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr3:46246600-46247600	Enhancers	GM12878-XiMat	blood
21	chr3:46246600-46247800	Active TSS	Adipose Nuclei	Adipose
22	chr3:46246600-46248200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:46246600-46249000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr3:46246800-46248000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:46246800-46249600	Active TSS	Brain Hippocampus Middle	brain
26	chr3:46247000-46247200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:46247000-46247400	Enhancers	Small Intestine	intestine
28	chr3:46247000-46247600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:46247000-46248600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:46247000-46249800	Active TSS	Fetal Muscle Leg	muscle
31	chr3:46247000-46251800	Enhancers	Primary B cells from peripheral blood	blood

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