Variant report

Variant	rs11006965
Chromosome Location	chr10:28550030-28550031
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	chr10:28548955..28550637-chr10:28589374..28591919,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10508736	0.83[CEU][hapmap]
rs10763646	0.83[CEU][hapmap]
rs10763647	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs10763648	0.83[CEU][hapmap]
rs10763649	0.83[CEU][hapmap]
rs10763650	0.82[CEU][hapmap]
rs10763654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10763655	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10763658	0.86[ASN][1000 genomes]
rs10826424	0.83[CEU][hapmap]
rs10826425	0.95[JPT][hapmap]
rs10826433	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826449	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11006917	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs11006946	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006950	0.87[JPT][hapmap]
rs11006956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006959	0.93[ASN][1000 genomes]
rs11006962	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11006970	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1144513	0.81[ASN][1000 genomes]
rs1148175	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12049636	0.83[CEU][hapmap]
rs12256403	0.82[CHB][hapmap]
rs1418757	0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1418759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17758855	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1870097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870098	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1937807	0.83[CEU][hapmap]
rs1937808	0.83[CEU][hapmap]
rs1937809	0.83[CEU][hapmap]
rs1953322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1953324	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2085471	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100615	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2100616	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124955	0.86[CHB][hapmap]
rs2290701	0.88[ASN][1000 genomes]
rs2607540	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2801833	0.83[CEU][hapmap]
rs2801835	0.83[CEU][hapmap]
rs2985535	0.83[CEU][hapmap]
rs2997210	0.83[CEU][hapmap]
rs3847388	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs61845911	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6481515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7072480	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7088465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7096944	0.83[CEU][hapmap]
rs7893311	0.83[CEU][hapmap]
rs7905490	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs7913970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9919516	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28519000-28552000	Weak transcription	Fetal Stomach	stomach
2	chr10:28535800-28551600	Weak transcription	Fetal Intestine Small	intestine
3	chr10:28537400-28552600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:28537600-28552600	Weak transcription	Primary T cells from cord blood	blood
5	chr10:28537800-28550200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr10:28542400-28552400	Weak transcription	Psoas Muscle	Psoas
7	chr10:28542800-28550200	Weak transcription	Aorta	Aorta
8	chr10:28544000-28552200	Weak transcription	Fetal Heart	heart
9	chr10:28544000-28555600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:28544200-28552400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr10:28544200-28554600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr10:28544600-28550200	Weak transcription	Pancreas	Pancrea
13	chr10:28545000-28550200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:28546200-28550200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:28546200-28552400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:28549200-28550800	Enhancers	Stomach Smooth Muscle	stomach
17	chr10:28549400-28550400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr10:28549400-28550600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr10:28549400-28550600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr10:28549400-28550800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr10:28549400-28551400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr10:28549400-28551600	Enhancers	Primary B cells from peripheral blood	blood
23	chr10:28549600-28552600	Weak transcription	Right Ventricle	heart
24	chr10:28549800-28550400	Enhancers	Primary B cells from cord blood	blood
25	chr10:28549800-28550400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr10:28549800-28550600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr10:28550000-28550400	Enhancers	GM12878-XiMat	blood
28	chr10:28550000-28550600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr10:28550000-28550600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:28550000-28550600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr10:28550000-28550600	Enhancers	Colon Smooth Muscle	Colon
32	chr10:28550000-28550600	Enhancers	Rectal Smooth Muscle	rectum
33	chr10:28550000-28552200	Enhancers	HepG2	liver

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