Variant report

Variant	rs16871291
Chromosome Location	chr6:11368793-11368794
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11343828..11346544-chr6:11366982..11368988,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10484453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10484454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12524463	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12525329	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12525704	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12525719	0.88[ASN][1000 genomes]
rs12526759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12527813	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16871294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16871306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4607428	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6903648	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6935901	0.84[YRI][hapmap]
rs73366863	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742703	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7746976	1.00[CHB][hapmap]
rs7752886	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7760294	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926314	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11355200-11370800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:11357200-11371200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:11357800-11370400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:11359400-11369800	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:11361200-11370600	Weak transcription	Thymus	Thymus
6	chr6:11364600-11369400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:11364600-11371200	Enhancers	HUVEC	blood vessel
8	chr6:11364600-11381200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:11364800-11370400	Weak transcription	Spleen	Spleen
10	chr6:11364800-11370800	Weak transcription	Placenta	Placenta
11	chr6:11365000-11370600	Weak transcription	Fetal Thymus	thymus
12	chr6:11365600-11374400	Weak transcription	Stomach Mucosa	stomach
13	chr6:11365600-11374800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:11365800-11369800	Weak transcription	Fetal Lung	lung
15	chr6:11366200-11369400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:11366400-11369200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr6:11366400-11369400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:11366800-11369000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:11366800-11369000	Enhancers	Fetal Intestine Large	intestine
20	chr6:11366800-11369400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:11366800-11369400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:11366800-11369600	Enhancers	NHEK	skin
23	chr6:11366800-11369800	Enhancers	HMEC	breast
24	chr6:11366800-11371000	Enhancers	Fetal Kidney	kidney
25	chr6:11367000-11369000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:11367000-11369400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:11367000-11369400	Enhancers	NH-A	brain
28	chr6:11367000-11370600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:11367000-11370800	Weak transcription	Esophagus	oesophagus
30	chr6:11367200-11368800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:11367200-11369000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:11367200-11369400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:11367200-11370000	Weak transcription	Brain Substantia Nigra	brain
34	chr6:11367200-11370200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:11367200-11370400	Weak transcription	Pancreas	Pancrea
36	chr6:11367600-11370200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:11367600-11372000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:11368000-11368800	Enhancers	Right Atrium	heart
39	chr6:11368000-11369400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr6:11368000-11370800	Weak transcription	Right Ventricle	heart
41	chr6:11368000-11371000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:11368200-11369200	Genic enhancers	GM12878-XiMat	blood
43	chr6:11368200-11370000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr6:11368200-11370000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:11368200-11370000	Weak transcription	Brain Anterior Caudate	brain
46	chr6:11368200-11370200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:11368200-11370400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:11368200-11370400	Weak transcription	Gastric	stomach
49	chr6:11368200-11370600	Weak transcription	Fetal Stomach	stomach
50	chr6:11368400-11369000	Weak transcription	Primary T cells from cord blood	blood

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