Variant report

Variant	rs9463971
Chromosome Location	chr6:53606001-53606002
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53598898..53601641-chr6:53603723..53606379,2	MCF-7	breast:
2	chr6:53603213..53606013-chr6:53606213..53607991,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL31-2	chr6:53605547-53606136	XLOC_005748
2	lnc-KLHL31-2	chr6:53605629-53606136	NONHSAT113194

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11759427	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11759473	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12662433	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663216	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs3003492	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs3003498	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs3813850	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4478409	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4486000	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4712042	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715421	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57853292	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62399939	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458956	0.95[ASN][1000 genomes]
rs6905563	0.82[JPT][hapmap]
rs7759593	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9463970	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9463975	0.94[EUR][1000 genomes]
rs9463976	0.95[EUR][1000 genomes]
rs9463996	0.84[JPT][hapmap]
rs9474643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9474647	1.00[CEU][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9474650	0.95[EUR][1000 genomes]
rs9474651	0.95[EUR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53599800-53606200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:53600800-53606200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:53601000-53606200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:53601200-53606200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:53601800-53613400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:53602200-53606400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:53602200-53614800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:53603000-53608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:53603000-53608800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:53603200-53608000	Weak transcription	NHEK	skin
12	chr6:53603200-53609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:53603600-53607800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:53603600-53608000	Weak transcription	Placenta	Placenta
15	chr6:53605200-53606600	Enhancers	Fetal Intestine Large	intestine
16	chr6:53605600-53606400	Enhancers	HepG2	liver
17	chr6:53605800-53606200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:53605800-53606200	Enhancers	Primary T cells from cord blood	blood
19	chr6:53605800-53606200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:53605800-53606200	Enhancers	Small Intestine	intestine
21	chr6:53605800-53606400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:53605800-53606400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:53605800-53606600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:53605800-53606600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:53605800-53606800	Flanking Active TSS	Dnd41	blood
26	chr6:53605800-53607000	Enhancers	Thymus	Thymus
27	chr6:53605800-53607200	Enhancers	Fetal Thymus	thymus
28	chr6:53606000-53606200	Enhancers	Fetal Intestine Small	intestine
29	chr6:53606000-53606400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:53606000-53606400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:53606000-53606600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr6:53606000-53606600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr6:53606000-53606800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:53606000-53606800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr6:53606000-53607000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr6:53606000-53607200	Enhancers	Primary neutrophils fromperipheralblood	blood

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