Variant report

Variant	rs6869512
Chromosome Location	chr5:118687375-118687376
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	chr5:118686914..118688782-chr5:118689065..118691768,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145779	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10059175	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10477585	0.85[AFR][1000 genomes]
rs10519585	0.85[JPT][hapmap]
rs1112247	0.91[YRI][hapmap]
rs13155880	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1396609	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17145230	0.85[JPT][hapmap]
rs17145265	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs250298	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs250299	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs250308	0.83[AFR][1000 genomes]
rs32653	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs32655	0.85[AFR][1000 genomes]
rs32657	0.85[AFR][1000 genomes]
rs32658	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs3797339	0.86[AFR][1000 genomes]
rs3797340	0.88[ASN][1000 genomes]
rs3797341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797343	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3813308	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs3920174	0.88[AFR][1000 genomes]
rs408095	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs67328001	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6863311	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6864305	0.91[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870253	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6876224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6877025	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6878879	0.85[JPT][hapmap]
rs6882237	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6884061	1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs6891084	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6896277	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6896553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6896559	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6897359	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73237292	0.98[ASN][1000 genomes]
rs73237297	0.94[ASN][1000 genomes]
rs73239278	0.87[ASN][1000 genomes]
rs73239280	0.87[ASN][1000 genomes]
rs7707470	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7731632	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs996934	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv599565	chr5:118661882-118691888	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882775	chr5:118669094-118691888	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118670800-118691000	Weak transcription	Aorta	Aorta
2	chr5:118671200-118695400	Weak transcription	A549	lung
3	chr5:118674200-118689000	Weak transcription	Esophagus	oesophagus
4	chr5:118674400-118689000	Weak transcription	Gastric	stomach
5	chr5:118676800-118689000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:118676800-118691400	Weak transcription	Lung	lung
7	chr5:118678000-118690600	Weak transcription	NHEK	skin
8	chr5:118679000-118690600	Weak transcription	Fetal Intestine Small	intestine
9	chr5:118679000-118690800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:118679800-118689400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:118680200-118690400	Weak transcription	Stomach Mucosa	stomach
12	chr5:118680200-118690600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:118680200-118690600	Weak transcription	Colonic Mucosa	Colon
14	chr5:118680400-118689000	Weak transcription	Placenta	Placenta
15	chr5:118680400-118690600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr5:118680800-118691000	Weak transcription	HSMMtube	muscle
17	chr5:118682000-118689200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:118682000-118689200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr5:118682000-118689200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:118682000-118689600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:118682200-118687800	Weak transcription	Fetal Thymus	thymus
22	chr5:118682200-118688200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:118682200-118689600	Weak transcription	Pancreas	Pancrea
24	chr5:118682600-118687600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:118682600-118688200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:118682600-118689000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:118682600-118689400	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr5:118682600-118689600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:118682600-118690600	Weak transcription	Thymus	Thymus
30	chr5:118682600-118693600	Weak transcription	Dnd41	blood
31	chr5:118683000-118688200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:118683600-118689000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:118683600-118689200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr5:118683800-118688000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:118683800-118689000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:118683800-118689800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:118683800-118689800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:118684000-118687800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr5:118684000-118688800	Weak transcription	Adipose Nuclei	Adipose
40	chr5:118684000-118688800	Weak transcription	Fetal Kidney	kidney
41	chr5:118684000-118690600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:118684000-118690800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:118684000-118691000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:118684000-118691000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr5:118684000-118692800	Weak transcription	K562	blood
46	chr5:118684200-118688000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:118684200-118689000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:118684200-118689000	Weak transcription	NHDF-Ad	bronchial
49	chr5:118684200-118689400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:118684200-118690400	Weak transcription	Hela-S3	cervix

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