Variant report

Variant	rs62386571
Chromosome Location	chr6:4789277-4789278
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4774936..4777199-chr6:4788444..4791160,3	MCF-7	breast:
2	chr6:4789235..4792155-chr6:4793481..4795463,2	MCF-7	breast:
3	chr6:4778081..4781516-chr6:4787216..4791667,5	MCF-7	breast:
4	chr6:4788250..4792483-chr6:4794003..4797255,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236336	Chromatin interaction
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2179269	0.86[ASN][1000 genomes]
rs61610972	0.81[ASN][1000 genomes]
rs62386575	0.86[ASN][1000 genomes]
rs62386578	0.81[ASN][1000 genomes]
rs62386582	0.81[ASN][1000 genomes]
rs62386584	0.86[ASN][1000 genomes]
rs62386585	0.86[ASN][1000 genomes]
rs62386587	0.86[ASN][1000 genomes]
rs62386590	0.86[ASN][1000 genomes]
rs62386591	0.86[ASN][1000 genomes]
rs62386593	0.86[ASN][1000 genomes]
rs62386594	0.86[ASN][1000 genomes]
rs62386612	0.86[ASN][1000 genomes]
rs62386614	0.86[ASN][1000 genomes]
rs6918626	0.81[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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3429586	chr6:4719363-4792438	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1015888	chr6:4787784-4883663	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4778400-4789600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:4778400-4790000	Weak transcription	Stomach Mucosa	stomach
3	chr6:4778600-4790000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:4781400-4794000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:4781400-4794400	Weak transcription	NHLF	lung
6	chr6:4781600-4797800	Weak transcription	Hela-S3	cervix
7	chr6:4781800-4790000	Weak transcription	Fetal Lung	lung
8	chr6:4781800-4794200	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:4782000-4790600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:4782000-4794400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:4782000-4797800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:4782600-4791400	Weak transcription	Fetal Heart	heart
13	chr6:4782800-4789600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:4782800-4790600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:4783000-4789600	Weak transcription	Small Intestine	intestine
16	chr6:4783000-4791400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:4783400-4789600	Weak transcription	Colonic Mucosa	Colon
18	chr6:4785200-4790000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:4785400-4789600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:4785400-4789600	Weak transcription	Fetal Intestine Small	intestine
21	chr6:4785400-4794400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:4785600-4789800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr6:4785600-4789800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:4785600-4789800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:4785600-4790000	Weak transcription	Fetal Stomach	stomach
26	chr6:4786000-4790000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:4786000-4790800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:4786200-4789600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:4786200-4790000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:4786200-4792000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:4786600-4793400	Weak transcription	A549	lung
32	chr6:4787000-4790200	Enhancers	Primary T cells fromperipheralblood	blood
33	chr6:4787200-4790800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
34	chr6:4787200-4791400	Weak transcription	Thymus	Thymus
35	chr6:4787200-4794400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:4787400-4790000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:4787400-4791400	Weak transcription	HepG2	liver
38	chr6:4787400-4793200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:4787400-4794000	Weak transcription	Colon Smooth Muscle	Colon
40	chr6:4787400-4808800	Weak transcription	Aorta	Aorta
41	chr6:4787600-4790400	Weak transcription	Fetal Kidney	kidney
42	chr6:4787600-4794400	Weak transcription	NHEK	skin
43	chr6:4787800-4789400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:4788000-4790000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:4788200-4790200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:4788200-4790400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:4788400-4790200	Enhancers	Fetal Muscle Leg	muscle
48	chr6:4788600-4790200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:4788800-4790000	Enhancers	Left Ventricle	heart
50	chr6:4788800-4790000	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links