Variant report

Variant	rs6879652
Chromosome Location	chr5:95227462-95227463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95222676..95225284-chr5:95226303..95229080,3	K562	blood:
2	chr5:95218349..95221486-chr5:95224324..95227675,3	K562	blood:
3	chr5:95224998..95227619-chr5:95296041..95298177,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118985	Chromatin interaction
ENSG00000251314	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10035477	1.00[CEU][hapmap];0.90[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10052503	0.85[YRI][hapmap]
rs10069748	1.00[CEU][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10070197	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1043381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057963	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1057964	1.00[CEU][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11135441	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs11135442	1.00[CEU][hapmap];0.90[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11738768	0.99[EUR][1000 genomes]
rs11738945	0.84[CEU][hapmap]
rs11739652	0.99[EUR][1000 genomes]
rs11741563	0.97[EUR][1000 genomes]
rs11741590	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11742959	0.84[CEU][hapmap]
rs11744881	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs13361341	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13361837	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1423268	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1423269	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1458017	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1458018	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1458019	0.95[EUR][1000 genomes]
rs147295	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs154460	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17085231	1.00[CEU][hapmap];0.90[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17085249	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17085266	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1841010	1.00[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2015159	0.91[EUR][1000 genomes]
rs2042340	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2270554	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2348984	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2546191	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2547997	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2548594	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2829	0.95[EUR][1000 genomes]
rs3777163	0.80[YRI][hapmap]
rs3777178	0.83[YRI][hapmap]
rs3777179	0.84[CEU][hapmap]
rs3777182	0.89[EUR][1000 genomes]
rs3777183	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs3777184	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3777185	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3777188	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3777189	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3777190	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3777192	0.95[EUR][1000 genomes]
rs3777193	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3777194	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3777196	1.00[CEU][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3777197	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3777200	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs3777201	0.99[EUR][1000 genomes]
rs3777202	0.99[EUR][1000 genomes]
rs3777203	0.99[EUR][1000 genomes]
rs3777204	1.00[CEU][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3777208	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3815768	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs4563648	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4642392	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56156268	0.97[EUR][1000 genomes]
rs56219066	0.99[EUR][1000 genomes]
rs6556893	1.00[CEU][hapmap];0.90[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6877329	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6885567	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6889029	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6890954	1.00[CEU][hapmap];0.90[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7700895	0.83[YRI][hapmap]
rs7702674	0.99[EUR][1000 genomes]
rs7716691	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs889302	0.95[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9314162	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs967546	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9986236	0.94[EUR][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	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95213000-95244600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:95214400-95234200	Weak transcription	Fetal Brain Female	brain
3	chr5:95214400-95247800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:95214400-95251800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:95214600-95230400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:95215000-95230200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:95215200-95234200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:95215800-95244600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:95217800-95230000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:95218000-95231000	Weak transcription	Right Atrium	heart
11	chr5:95218000-95242200	Weak transcription	Spleen	Spleen
12	chr5:95218200-95231600	Weak transcription	Fetal Heart	heart
13	chr5:95218200-95246200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:95219200-95229600	Weak transcription	Esophagus	oesophagus
15	chr5:95219800-95244400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:95220000-95242000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:95220000-95245200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:95220200-95230600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:95220200-95235400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:95220400-95236800	Strong transcription	HMEC	breast
21	chr5:95220600-95236200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:95220600-95243200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:95220800-95234000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:95220800-95235400	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr5:95220800-95235600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:95220800-95237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:95220800-95237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:95220800-95240800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:95221000-95230000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:95221000-95236600	Strong transcription	NH-A	brain
31	chr5:95221200-95227600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr5:95221200-95232400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:95221400-95230800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:95221400-95236200	Strong transcription	HSMM	muscle
35	chr5:95221600-95235800	Strong transcription	Osteobl	bone
36	chr5:95221600-95252200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr5:95221800-95227600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:95221800-95230000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:95221800-95230600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:95221800-95232400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr5:95221800-95233600	Weak transcription	Fetal Lung	lung
42	chr5:95222000-95241600	Strong transcription	GM12878-XiMat	blood
43	chr5:95222000-95252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:95222400-95229600	Weak transcription	Fetal Stomach	stomach
45	chr5:95222800-95232600	Strong transcription	NHLF	lung
46	chr5:95222800-95235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:95223000-95259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:95223400-95237600	Strong transcription	Placenta	Placenta
49	chr5:95223600-95227600	Strong transcription	Adipose Nuclei	Adipose
50	chr5:95223800-95228800	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links