Variant report

Variant	rs13220665
Chromosome Location	chr6:53603347-53603348
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53603213..53606013-chr6:53606213..53607991,3	MCF-7	breast:
2	chr17:56708938..56710691-chr6:53601479..53604353,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL31-2	chr6:53603240-53603794	NONHSAT113194

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10948779	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs11755346	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745462	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2820215	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2820216	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap]
rs3000996	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3000997	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3000999	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3001000	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3001001	0.88[EUR][1000 genomes]
rs3001002	0.86[EUR][1000 genomes]
rs3001009	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs3001010	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003489	0.85[EUR][1000 genomes]
rs3003491	0.85[EUR][1000 genomes]
rs3003493	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs3003500	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3003501	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34165049	0.94[EUR][1000 genomes]
rs34861916	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34880762	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35389351	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35517171	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35756855	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236113	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs4265033	0.86[EUR][1000 genomes]
rs4276502	0.88[EUR][1000 genomes]
rs4286781	0.85[EUR][1000 genomes]
rs4321822	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4326237	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4336450	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4351263	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs4382260	0.85[EUR][1000 genomes]
rs4398733	0.85[EUR][1000 genomes]
rs4437471	0.84[EUR][1000 genomes]
rs4484515	0.85[EUR][1000 genomes]
rs4489155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4591854	0.85[EUR][1000 genomes]
rs4615391	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4712048	0.85[EUR][1000 genomes]
rs4712049	0.85[EUR][1000 genomes]
rs4715424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715426	0.85[EUR][1000 genomes]
rs59641455	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60035355	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458957	0.89[EUR][1000 genomes]
rs6458958	0.86[EUR][1000 genomes]
rs6458959	0.86[EUR][1000 genomes]
rs6458961	0.84[EUR][1000 genomes]
rs6458962	0.84[EUR][1000 genomes]
rs6458965	0.85[EUR][1000 genomes]
rs6458966	0.85[EUR][1000 genomes]
rs6458969	0.85[EUR][1000 genomes]
rs6458972	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs6650996	0.84[EUR][1000 genomes]
rs6899752	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920743	0.86[EUR][1000 genomes]
rs6924025	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs6925836	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926478	0.85[EUR][1000 genomes]
rs6937901	0.85[EUR][1000 genomes]
rs71555560	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742524	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs7739965	0.85[EUR][1000 genomes]
rs7753504	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7754791	0.85[EUR][1000 genomes]
rs7759946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762883	0.84[EUR][1000 genomes]
rs7763081	0.85[EUR][1000 genomes]
rs7763147	0.86[EUR][1000 genomes]
rs7769893	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9296719	0.85[EUR][1000 genomes]
rs9296721	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9367544	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs9370235	0.85[EUR][1000 genomes]
rs9370239	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs9382234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382237	0.89[EUR][1000 genomes]
rs9395886	0.92[CEU][hapmap];1.00[CHB][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	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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53596000-53605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:53597200-53604000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:53599800-53606200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:53600000-53605800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:53600800-53603600	Enhancers	Dnd41	blood
6	chr6:53600800-53606200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:53601000-53606000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:53601000-53606200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:53601200-53605800	Weak transcription	Primary T cells from cord blood	blood
10	chr6:53601200-53605800	Weak transcription	Thymus	Thymus
11	chr6:53601200-53606000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:53601200-53606000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:53601200-53606000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:53601200-53606000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr6:53601200-53606200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:53601800-53603400	Enhancers	Fetal Intestine Large	intestine
18	chr6:53601800-53603400	Enhancers	HepG2	liver
19	chr6:53601800-53603600	Enhancers	Fetal Intestine Small	intestine
20	chr6:53601800-53613400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:53602000-53603600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr6:53602200-53606400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:53602200-53614800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:53602600-53603400	Enhancers	Fetal Thymus	thymus
25	chr6:53602600-53603600	Enhancers	Placenta	Placenta
26	chr6:53602800-53605800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:53603000-53608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:53603000-53608800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:53603200-53608000	Weak transcription	NHEK	skin
30	chr6:53603200-53609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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