Variant report

Variant	rs9382252
Chromosome Location	chr6:53771857-53771858
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	chr6:53768489..53771106-chr6:53771711..53773800,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1076701	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1076702	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12526194	0.82[AMR][1000 genomes]
rs13216331	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2073020	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2076495	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2294789	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2294790	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2294791	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3777661	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4455653	0.98[ASN][1000 genomes]
rs4516937	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs4563705	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6903399	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6934324	0.89[JPT][hapmap]
rs7749273	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7763482	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7776124	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9349685	0.93[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9357776	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9357778	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370233	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370241	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370244	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9370246	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382235	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9382238	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382241	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382243	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382244	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382246	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382248	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9382253	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382254	0.92[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382256	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382257	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9395878	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9395881	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9474646	0.81[CHB][hapmap];0.85[JPT][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	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:53754800-53775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:53754800-53779800	Weak transcription	NHLF	lung
4	chr6:53755000-53779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:53758000-53775600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
8	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
9	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
12	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
13	chr6:53760600-53773000	Strong transcription	Dnd41	blood
14	chr6:53760600-53778800	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:53761000-53782000	Weak transcription	Fetal Kidney	kidney
17	chr6:53761000-53782800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:53761400-53776400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:53761400-53787400	Weak transcription	HMEC	breast
21	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
23	chr6:53761800-53772400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr6:53761800-53777000	Strong transcription	Fetal Thymus	thymus
25	chr6:53761800-53786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:53762000-53774000	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr6:53762000-53775600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
30	chr6:53762200-53786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:53762800-53775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:53763000-53772200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:53764000-53772000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:53764000-53772000	Strong transcription	HSMMtube	muscle
35	chr6:53764200-53772000	Strong transcription	Fetal Intestine Small	intestine
36	chr6:53764400-53784600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:53766200-53772000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:53766800-53773000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:53767400-53772000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:53767400-53772000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr6:53767600-53772000	Strong transcription	NHEK	skin
42	chr6:53767600-53772400	Strong transcription	Primary T cells from cord blood	blood
43	chr6:53768000-53774600	Weak transcription	HUVEC	blood vessel
44	chr6:53768400-53772400	Strong transcription	Placenta	Placenta
45	chr6:53768600-53772000	Strong transcription	Colonic Mucosa	Colon
46	chr6:53768600-53785000	Weak transcription	Primary B cells from cord blood	blood
47	chr6:53768800-53775600	Weak transcription	Brain Germinal Matrix	brain
48	chr6:53768800-53778600	Weak transcription	Aorta	Aorta
49	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:53769000-53785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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