Variant report

Variant	rs62396374
Chromosome Location	chr6:38578769-38578770
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38571505..38574322-chr6:38577217..38578879,2	K562	blood:
2	chr6:38577291..38580074-chr6:38606571..38609057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183826	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13194484	1.00[AFR][1000 genomes]
rs16890840	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2748160	1.00[AFR][1000 genomes]
rs2894415	0.82[EUR][1000 genomes]
rs2894416	0.82[EUR][1000 genomes]
rs3778443	0.82[EUR][1000 genomes]
rs58458015	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60227349	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62396375	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62396376	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62396378	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs62396379	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62396381	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62396382	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62396385	0.82[EUR][1000 genomes]
rs62397716	0.87[AMR][1000 genomes]
rs62399161	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72849175	1.00[AFR][1000 genomes]
rs72852702	1.00[AFR][1000 genomes]
rs72855194	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38556000-38580400	Weak transcription	Ovary	ovary
2	chr6:38560800-38580000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr6:38560800-38580200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:38562200-38580000	Weak transcription	Aorta	Aorta
5	chr6:38562800-38579800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:38564000-38580400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:38565400-38589200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:38565800-38583200	Weak transcription	Primary T cells from cord blood	blood
9	chr6:38565800-38583600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:38567800-38580400	Weak transcription	Right Ventricle	heart
11	chr6:38568200-38580000	Weak transcription	Psoas Muscle	Psoas
12	chr6:38568200-38584200	Weak transcription	Primary B cells from cord blood	blood
13	chr6:38571000-38580000	Weak transcription	Small Intestine	intestine
14	chr6:38571600-38581800	Weak transcription	Left Ventricle	heart
15	chr6:38572000-38591600	Weak transcription	Fetal Intestine Small	intestine
16	chr6:38572600-38579800	Weak transcription	NHLF	lung
17	chr6:38572800-38579800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:38572800-38581800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:38573000-38579800	Weak transcription	HSMMtube	muscle
20	chr6:38576200-38579800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:38577600-38580800	Enhancers	Fetal Lung	lung
22	chr6:38577800-38580400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:38578000-38581400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:38578000-38582600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:38578400-38579200	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:38578400-38579200	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr6:38578400-38579800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:38578400-38579800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:38578400-38580000	Weak transcription	NH-A	brain
30	chr6:38578400-38581000	Enhancers	NHDF-Ad	bronchial
31	chr6:38578600-38578800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:38578600-38579000	Weak transcription	Osteobl	bone
33	chr6:38578600-38579600	Weak transcription	Stomach Mucosa	stomach
34	chr6:38578600-38579800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:38578600-38581600	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links