Variant report

Variant	rs6695671
Chromosome Location	chr1:86859216-86859217
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86858845..86860398-chr1:86869035..86871244,2	K562	blood:
2	chr1:86847598..86849300-chr1:86857540..86859309,2	MCF-7	breast:
3	chr1:86854491..86856100-chr1:86858979..86861323,2	K562	blood:
4	chr1:86856582..86859443-chr1:86866472..86868164,2	K562	blood:

Variant related genes	Relation type
ENSG00000231349	Chromatin interaction
ENSG00000122417	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10493789	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10747328	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10873777	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10873782	0.84[CEU][hapmap]
rs1158505	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1182102	0.96[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1334143	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1334145	0.88[CEU][hapmap]
rs1334146	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1334147	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1334148	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs166626	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs166627	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17129078	0.83[ASN][1000 genomes]
rs175363	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs185655	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs187971	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1931363	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2104963	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2151708	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2151709	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2250857	0.85[CHB][hapmap]
rs272491	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272492	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272494	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272498	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272504	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272507	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272510	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272511	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272516	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765975	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs405424	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4288573	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61804060	0.83[ASN][1000 genomes]
rs883200	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
2	chr1:86820400-86860200	Weak transcription	NHEK	skin
3	chr1:86836600-86860800	Weak transcription	Aorta	Aorta
4	chr1:86840600-86859600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:86841000-86859800	Weak transcription	HSMM	muscle
6	chr1:86841600-86859800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:86843400-86860800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:86843600-86860600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:86843600-86860800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:86844800-86861000	Weak transcription	Fetal Intestine Small	intestine
11	chr1:86845000-86859400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:86845000-86860200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:86845000-86860600	Weak transcription	Fetal Thymus	thymus
14	chr1:86845000-86860800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:86845200-86859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:86846600-86860400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:86848800-86861000	Weak transcription	Primary B cells from cord blood	blood
18	chr1:86849200-86860200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:86849200-86860800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:86851800-86859800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:86852400-86860600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:86855600-86859600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:86855600-86860200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:86855600-86860800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:86855600-86860800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:86855800-86859600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:86855800-86860800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:86855800-86861000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:86856200-86860600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr1:86856600-86859600	Weak transcription	Thymus	Thymus
31	chr1:86857200-86861000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:86857800-86860200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:86858200-86859600	Enhancers	Dnd41	blood
34	chr1:86858400-86860800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:86858600-86859600	Enhancers	Brain Hippocampus Middle	brain
36	chr1:86858600-86859600	Enhancers	NHDF-Ad	bronchial
37	chr1:86858600-86859800	Enhancers	Fetal Heart	heart
38	chr1:86858600-86860800	Enhancers	Primary T cells from cord blood	blood
39	chr1:86858600-86860800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:86858600-86860800	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr1:86858800-86859400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr1:86858800-86859400	Enhancers	GM12878-XiMat	blood
43	chr1:86858800-86860000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:86858800-86860800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr1:86858800-86860800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:86858800-86860800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr1:86858800-86860800	Enhancers	Adipose Nuclei	Adipose
48	chr1:86858800-86861000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:86859000-86859400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:86859000-86860000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links