Variant report

Variant	rs2373154
Chromosome Location	chr3:46171098-46171099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46171083..46172669-chr3:46203226..46205309,3	MCF-7	breast:
2	chr3:46169290..46171223-chr3:46177395..46178997,2	K562	blood:
3	chr3:46161021..46162671-chr3:46170985..46172785,2	K562	blood:

Variant related genes	Relation type
ENSG00000183625	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1072755	0.92[CEU][hapmap]
rs11130080	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs11130085	0.89[ASN][1000 genomes]
rs11130086	0.90[ASN][1000 genomes]
rs1118879	0.87[ASN][1000 genomes]
rs11917890	0.89[ASN][1000 genomes]
rs11929281	0.89[ASN][1000 genomes]
rs12485978	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12495073	0.92[CEU][hapmap]
rs12496322	0.89[ASN][1000 genomes]
rs12629632	0.87[ASN][1000 genomes]
rs12630101	0.92[CEU][hapmap]
rs12635657	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs12637023	0.88[ASN][1000 genomes]
rs12639598	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs13060901	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs13065737	0.87[ASN][1000 genomes]
rs13066048	0.92[CEU][hapmap]
rs13073861	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs13077099	0.89[ASN][1000 genomes]
rs13077923	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13078053	0.92[ASN][1000 genomes]
rs13082280	0.86[ASN][1000 genomes]
rs13434029	0.86[ASN][1000 genomes]
rs13434336	0.82[ASN][1000 genomes]
rs1392290	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1491959	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1546077	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1546078	0.85[ASN][1000 genomes]
rs1552489	0.92[CEU][hapmap]
rs1602579	0.87[ASN][1000 genomes]
rs1604069	0.81[ASN][1000 genomes]
rs17078577	0.88[ASN][1000 genomes]
rs1909596	0.81[ASN][1000 genomes]
rs1976366	0.85[ASN][1000 genomes]
rs1976367	0.85[ASN][1000 genomes]
rs2054866	0.92[CEU][hapmap]
rs2131091	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs2220678	0.90[ASN][1000 genomes]
rs2373150	0.86[ASN][1000 genomes]
rs2373151	0.86[ASN][1000 genomes]
rs2373153	0.93[ASN][1000 genomes]
rs34067839	0.93[ASN][1000 genomes]
rs35359253	0.87[ASN][1000 genomes]
rs35462017	0.87[ASN][1000 genomes]
rs35567508	0.92[ASN][1000 genomes]
rs36111470	0.93[ASN][1000 genomes]
rs3774634	0.92[CEU][hapmap]
rs3774639	0.92[CEU][hapmap]
rs3796375	0.96[CEU][hapmap]
rs3851347	0.86[CHB][hapmap]
rs4318588	0.86[ASN][1000 genomes]
rs4535265	0.92[CEU][hapmap]
rs4682806	0.83[ASN][1000 genomes]
rs4682809	0.85[ASN][1000 genomes]
rs4682810	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4683157	0.92[CEU][hapmap]
rs4683175	0.88[ASN][1000 genomes]
rs4683178	0.89[ASN][1000 genomes]
rs56307311	0.93[ASN][1000 genomes]
rs59521415	0.87[ASN][1000 genomes]
rs61079448	0.87[ASN][1000 genomes]
rs6441944	0.87[ASN][1000 genomes]
rs6764042	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs6772051	0.85[EUR][1000 genomes]
rs6776028	0.85[ASN][1000 genomes]
rs6780163	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs6784214	0.85[ASN][1000 genomes]
rs6794103	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6794475	0.91[ASN][1000 genomes]
rs6795629	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6800484	0.83[ASN][1000 genomes]
rs6808074	0.85[EUR][1000 genomes]
rs6809381	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs730983	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs737452	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs751552	0.96[CEU][hapmap]
rs751553	0.96[CEU][hapmap]
rs7610518	0.87[ASN][1000 genomes]
rs7623460	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs7631598	0.81[ASN][1000 genomes]
rs7643426	0.81[CHB][hapmap]
rs9311386	0.81[ASN][1000 genomes]
rs9311387	0.81[ASN][1000 genomes]
rs936938	0.92[CEU][hapmap]
rs9637425	0.88[ASN][1000 genomes]
rs9824886	0.90[CHB][hapmap]
rs9870445	0.81[ASN][1000 genomes]
rs9876587	0.81[ASN][1000 genomes]
rs9990063	0.83[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2373154	UBA7	cis	parietal	SCAN
rs2373154	CXCR6	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46166200-46171200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:46166600-46172600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:46166800-46171400	Weak transcription	Placenta	Placenta
4	chr3:46167000-46171800	Weak transcription	Adipose Nuclei	Adipose
5	chr3:46167000-46175600	Weak transcription	Fetal Lung	lung
6	chr3:46168800-46178200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:46169000-46172600	Enhancers	Dnd41	blood
8	chr3:46169800-46173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:46170000-46177200	Enhancers	Fetal Thymus	thymus
10	chr3:46170600-46172800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:46170800-46171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:46170800-46171800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:46170800-46171800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:46170800-46171800	Enhancers	Spleen	Spleen
15	chr3:46170800-46172000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:46170800-46172000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr3:46170800-46172000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:46170800-46172600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:46170800-46174200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr3:46171000-46171200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:46171000-46171400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:46171000-46171600	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr3:46171000-46171600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:46171000-46171600	Enhancers	Thymus	Thymus
25	chr3:46171000-46171800	Enhancers	Primary T cells from cord blood	blood
26	chr3:46171000-46171800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr3:46171000-46171800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr3:46171000-46171800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:46171000-46171800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:46171000-46171800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr3:46171000-46172200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:46171000-46172800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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