Variant report

Variant	rs11955860
Chromosome Location	chr5:52329341-52329342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52313064..52315275-chr5:52327348..52329688,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10051913	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10068849	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12520747	0.82[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs1421933	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1421938	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2056403	0.94[ASN][1000 genomes]
rs2112290	0.80[AMR][1000 genomes]
rs2216729	0.85[CEU][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs2406598	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs26678	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212434	0.88[AFR][1000 genomes]
rs3212452	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3212469	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3212476	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3212530	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3797499	0.91[AFR][1000 genomes]
rs7719848	0.84[CEU][hapmap]
rs7731858	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736005	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs988557	0.84[CEU][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs988558	0.85[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs988559	0.88[AFR][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	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
5	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
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52307000-52333800	Weak transcription	Gastric	stomach
2	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:52317600-52333600	Weak transcription	Colonic Mucosa	Colon
4	chr5:52318400-52331800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:52322200-52333200	Weak transcription	Fetal Stomach	stomach
6	chr5:52323600-52332600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:52324200-52334200	Weak transcription	Spleen	Spleen
8	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
9	chr5:52324600-52332400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:52326400-52329400	Enhancers	Dnd41	blood
11	chr5:52326400-52329400	Enhancers	Hela-S3	cervix
12	chr5:52326800-52329400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr5:52327600-52333000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:52327800-52329400	Enhancers	Osteobl	bone
15	chr5:52327800-52330400	Weak transcription	Fetal Kidney	kidney
16	chr5:52327800-52332200	Weak transcription	Esophagus	oesophagus
17	chr5:52327800-52333800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:52327800-52334400	Weak transcription	Pancreas	Pancrea
19	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:52328000-52332600	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:52328000-52332800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:52328000-52333000	Weak transcription	HSMM	muscle
23	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
24	chr5:52328200-52332000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:52328400-52330400	Weak transcription	Brain Substantia Nigra	brain
26	chr5:52328400-52332000	Weak transcription	Brain Hippocampus Middle	brain
27	chr5:52328400-52333000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:52328400-52333000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:52328400-52333800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:52328600-52329400	Genic enhancers	NHEK	skin
31	chr5:52328600-52335200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr5:52328800-52330200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:52328800-52330200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:52328800-52330200	Weak transcription	Fetal Lung	lung
35	chr5:52328800-52331800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:52328800-52331800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:52328800-52332000	Weak transcription	NH-A	brain
38	chr5:52328800-52332600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:52328800-52333200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:52328800-52335800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
42	chr5:52329000-52330400	Strong transcription	HepG2	liver
43	chr5:52329000-52331800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:52329000-52331800	Weak transcription	NHLF	lung
45	chr5:52329000-52332800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:52329000-52334200	Weak transcription	Lung	lung
47	chr5:52329200-52329800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:52329200-52330000	Weak transcription	HMEC	breast
49	chr5:52329200-52330200	Weak transcription	A549	lung
50	chr5:52329200-52331800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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