Variant report

Variant	rs6859171
Chromosome Location	chr5:52241438-52241439
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	chr5:52239227..52240957-chr5:52240958..52243466,2	MCF-7	breast:
2	chr5:52240942..52242706-chr5:52367816..52370164,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10513004	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940280	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738606	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11739571	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742694	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11742813	0.87[EUR][1000 genomes]
rs11745309	0.81[YRI][hapmap]
rs11748504	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749081	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12186544	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13156420	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13165509	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13179969	0.86[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180488	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421943	0.86[EUR][1000 genomes]
rs3212383	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs3212656	0.83[EUR][1000 genomes]
rs34288275	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34352729	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34512129	0.86[EUR][1000 genomes]
rs34865297	0.86[EUR][1000 genomes]
rs35597318	0.86[EUR][1000 genomes]
rs35657730	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35862618	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35926366	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865755	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[GIH][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap]
rs7702766	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7713782	0.83[EUR][1000 genomes]
rs9791046	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv1794366	chr5:52240421-52249476	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
2	chr5:52211600-52244400	Weak transcription	HepG2	liver
3	chr5:52218600-52242200	Weak transcription	Fetal Kidney	kidney
4	chr5:52220000-52243000	Weak transcription	Gastric	stomach
5	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:52224200-52244600	Weak transcription	Primary T cells from cord blood	blood
8	chr5:52229000-52246600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:52231600-52245400	Weak transcription	Colonic Mucosa	Colon
10	chr5:52232800-52249800	Weak transcription	Left Ventricle	heart
11	chr5:52235400-52243200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:52238800-52252200	Strong transcription	Liver	Liver
13	chr5:52240000-52245400	Weak transcription	Placenta	Placenta
14	chr5:52240000-52249800	Weak transcription	Aorta	Aorta
15	chr5:52240000-52253000	Weak transcription	Right Ventricle	heart
16	chr5:52240000-52253400	Weak transcription	Esophagus	oesophagus
17	chr5:52240000-52253600	Weak transcription	Lung	lung
18	chr5:52240200-52244200	Weak transcription	Fetal Lung	lung
19	chr5:52240200-52244200	Weak transcription	Fetal Stomach	stomach
20	chr5:52240200-52247000	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:52240200-52251800	Weak transcription	Fetal Intestine Small	intestine
22	chr5:52240200-52253400	Weak transcription	Spleen	Spleen
23	chr5:52240400-52251800	Weak transcription	Fetal Intestine Large	intestine
24	chr5:52240600-52241600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:52240600-52241600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:52240600-52242200	Active TSS	HMEC	breast
27	chr5:52240600-52244200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr5:52240800-52241600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr5:52240800-52241600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:52240800-52241600	Active TSS	Right Atrium	heart
31	chr5:52240800-52241600	Active TSS	NHEK	skin
32	chr5:52240800-52241800	Flanking Active TSS	HUVEC	blood vessel
33	chr5:52240800-52242000	Active TSS	A549	lung
34	chr5:52240800-52242400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:52240800-52242400	Enhancers	Hela-S3	cervix
36	chr5:52240800-52242400	Active TSS	NHLF	lung
37	chr5:52241000-52241600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:52241000-52241600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:52241200-52242000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:52241200-52242200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:52241200-52242200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr5:52241200-52243200	Weak transcription	HSMM	muscle
43	chr5:52241200-52243200	Weak transcription	NH-A	brain
44	chr5:52241200-52243400	Enhancers	Rectal Smooth Muscle	rectum
45	chr5:52241200-52243600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:52241200-52243600	Weak transcription	Dnd41	blood
47	chr5:52241200-52245600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:52241200-52252000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr5:52241400-52241600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:52241400-52241600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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