Variant report

Variant	rs9496961
Chromosome Location	chr6:144725222-144725223
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144682093..144683894-chr6:144723958..144726060,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11965745	1.00[ASN][1000 genomes]
rs2223428	1.00[ASN][1000 genomes]
rs2328570	1.00[ASN][1000 genomes]
rs4546509	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57580585	1.00[ASN][1000 genomes]
rs59893699	1.00[ASN][1000 genomes]
rs6902637	1.00[ASN][1000 genomes]
rs6910059	1.00[ASN][1000 genomes]
rs6920634	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs6936691	1.00[ASN][1000 genomes]
rs7748278	1.00[ASN][1000 genomes]
rs7755700	1.00[ASN][1000 genomes]
rs9321973	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9484868	1.00[ASN][1000 genomes]
rs9484871	1.00[ASN][1000 genomes]
rs9484873	1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs9496951	0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[ASN][1000 genomes]
rs9496952	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9496953	0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[ASN][1000 genomes]
rs9496954	1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs9496965	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1023014	chr6:144717963-144806691	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv516523	chr6:144719765-144728332	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv527525	chr6:144719765-144737670	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv886739	chr6:144719765-144796516	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144697200-144732600	Weak transcription	Gastric	stomach
2	chr6:144711800-144728000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:144712000-144726400	Weak transcription	HSMMtube	muscle
4	chr6:144712600-144732600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:144716800-144726400	Weak transcription	HUVEC	blood vessel
6	chr6:144716800-144729200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:144717000-144726800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:144717400-144729400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:144719200-144736200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:144719400-144726200	Weak transcription	Fetal Lung	lung
11	chr6:144719400-144727600	Weak transcription	Esophagus	oesophagus
12	chr6:144719400-144728200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:144719400-144730600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:144719400-144732400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:144719400-144737000	Weak transcription	Spleen	Spleen
16	chr6:144719600-144725800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:144719600-144728000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:144719600-144729200	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:144719600-144729200	Weak transcription	Left Ventricle	heart
20	chr6:144719600-144730600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:144719600-144732400	Weak transcription	Fetal Thymus	thymus
22	chr6:144719600-144732600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:144719600-144732600	Weak transcription	Thymus	Thymus
24	chr6:144719600-144732800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:144719600-144736200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:144719600-144736400	Weak transcription	HSMM	muscle
27	chr6:144719600-144744000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:144719800-144726000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:144719800-144726200	Weak transcription	Dnd41	blood
30	chr6:144719800-144732400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:144719800-144732400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:144719800-144743000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:144719800-144744400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:144720000-144728000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:144720000-144728000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:144720000-144732600	Weak transcription	GM12878-XiMat	blood
37	chr6:144720000-144743200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr6:144720000-144758200	Weak transcription	Fetal Intestine Small	intestine
39	chr6:144720200-144744000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:144721000-144732400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:144721000-144736200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:144721200-144726400	Weak transcription	NHDF-Ad	bronchial
43	chr6:144721200-144732400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr6:144721400-144726200	Weak transcription	Fetal Stomach	stomach
45	chr6:144722000-144729400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:144722200-144726400	Weak transcription	NHLF	lung
47	chr6:144722400-144727000	Strong transcription	Primary B cells from cord blood	blood
48	chr6:144722400-144744000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr6:144722600-144725600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:144722600-144726200	Weak transcription	Fetal Kidney	kidney

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