Variant report

Variant	rs4457161
Chromosome Location	chr6:53606394-53606395
allele	C/T
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:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10456672	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758147	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216331	0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345397	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4373352	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4400206	0.82[CHB][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4404762	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4441952	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4516937	0.91[CHB][hapmap];0.82[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4563705	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4610551	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4712043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712044	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908232	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6921605	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6925356	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6934324	0.89[CHB][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7749273	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756512	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7763482	0.91[CHB][hapmap];0.82[JPT][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7776124	0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370233	0.80[AMR][1000 genomes]
rs9382235	0.91[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9382238	0.83[AMR][1000 genomes]
rs9382241	0.83[AMR][1000 genomes]
rs9395878	0.83[AMR][1000 genomes]
rs9474639	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9474640	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9474641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474646	0.91[CHB][hapmap];0.83[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9474649	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:53601800-53613400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:53602200-53606400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:53602200-53614800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:53603000-53608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:53603000-53608800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:53603200-53608000	Weak transcription	NHEK	skin
8	chr6:53603200-53609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:53603600-53607800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:53603600-53608000	Weak transcription	Placenta	Placenta
11	chr6:53605200-53606600	Enhancers	Fetal Intestine Large	intestine
12	chr6:53605600-53606400	Enhancers	HepG2	liver
13	chr6:53605800-53606400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:53605800-53606400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:53605800-53606600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:53605800-53606600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:53605800-53606800	Flanking Active TSS	Dnd41	blood
18	chr6:53605800-53607000	Enhancers	Thymus	Thymus
19	chr6:53605800-53607200	Enhancers	Fetal Thymus	thymus
20	chr6:53606000-53606400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:53606000-53606400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:53606000-53606600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr6:53606000-53606600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:53606000-53606800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:53606000-53606800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr6:53606000-53607000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr6:53606000-53607200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr6:53606200-53606400	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr6:53606200-53606400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr6:53606200-53606600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr6:53606200-53606600	Enhancers	Primary B cells from cord blood	blood
32	chr6:53606200-53606600	Enhancers	Primary T cells fromperipheralblood	blood
33	chr6:53606200-53606600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr6:53606200-53606600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:53606200-53606600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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