Variant report

Variant	rs960945
Chromosome Location	chr6:11188012-11188013
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	chr6:11180911..11183612-chr6:11187245..11190194,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1007741	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209631	1.00[CHB][hapmap]
rs13849	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1803710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2146344	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208840	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327336	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3035	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34044517	1.00[ASN][1000 genomes]
rs4711193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713227	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713229	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456946	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906952	1.00[CHB][hapmap]
rs6912556	0.88[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923556	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923725	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935824	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739880	0.85[CEU][hapmap]
rs7746976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751344	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755052	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755536	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759674	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770498	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9283888	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295806	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368595	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941982	0.85[MEX][hapmap]
rs9468537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468556	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960944	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11172800-11195000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:11178400-11190000	Weak transcription	Brain Anterior Caudate	brain
3	chr6:11179000-11202200	Weak transcription	Brain Substantia Nigra	brain
4	chr6:11180200-11190200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:11180200-11194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:11180600-11194400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:11180800-11194800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:11181600-11196200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:11182000-11194000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:11182200-11188400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:11182200-11190000	Weak transcription	Fetal Lung	lung
12	chr6:11182400-11194000	Strong transcription	NH-A	brain
13	chr6:11182400-11195200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr6:11182600-11194800	Strong transcription	Primary B cells from cord blood	blood
15	chr6:11183000-11199000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr6:11183200-11195000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:11183400-11191800	Strong transcription	Fetal Thymus	thymus
18	chr6:11183400-11194000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:11183400-11194000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:11183400-11194000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:11183400-11194000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:11183400-11194600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:11183400-11194600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr6:11183400-11195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:11183600-11188200	Strong transcription	Osteobl	bone
26	chr6:11183600-11188400	Strong transcription	HSMM	muscle
27	chr6:11183600-11192400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:11183600-11194200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:11183800-11188200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:11183800-11188200	Strong transcription	HepG2	liver
31	chr6:11183800-11189400	Weak transcription	NHEK	skin
32	chr6:11183800-11194000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:11184000-11188800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:11184000-11192200	Strong transcription	Fetal Brain Female	brain
35	chr6:11184000-11192400	Strong transcription	Fetal Kidney	kidney
36	chr6:11184000-11192600	Strong transcription	Rectal Smooth Muscle	rectum
37	chr6:11184000-11194000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:11184000-11194000	Strong transcription	Primary T cells from cord blood	blood
39	chr6:11184000-11194000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:11184000-11194000	Strong transcription	Adipose Nuclei	Adipose
41	chr6:11184000-11194000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr6:11184000-11194000	Strong transcription	Thymus	Thymus
43	chr6:11184000-11194000	Strong transcription	HUVEC	blood vessel
44	chr6:11184000-11194200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:11184000-11194600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:11184200-11193800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:11184200-11194000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:11184400-11192200	Strong transcription	Fetal Muscle Leg	muscle
49	chr6:11184400-11192400	Strong transcription	GM12878-XiMat	blood
50	chr6:11184400-11193000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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