Variant report

Variant	rs62454509
Chromosome Location	chr7:19746009-19746010
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:19744052..19746655-chr7:19747190..19748728,2	MCF-7	breast:
2	chr7:19745274..19751651-chr7:20366071..20371531,8	MCF-7	breast:
3	chr7:19745589..19748453-chr7:19756261..19758585,2	K562	blood:
4	chr7:19745703..19748379-chr7:20271088..20273693,2	K562	blood:
5	chr7:19745703..19747865-chr7:20271912..20273693,2	K562	blood:

Variant related genes	Relation type
ENSG00000105849	Chromatin interaction
ENSG00000105855	Chromatin interaction
ENSG00000271133	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs56089097	0.92[EUR][1000 genomes]
rs56104650	0.92[EUR][1000 genomes]
rs62454500	0.90[EUR][1000 genomes]
rs62454501	0.92[EUR][1000 genomes]
rs62454508	0.88[EUR][1000 genomes]
rs73081060	0.90[EUR][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	nsv1018601	chr7:19272360-20008881	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1033223	chr7:19682192-20461375	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv538795	chr7:19682192-20461375	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv524807	chr7:19714156-19803925	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19730400-19747400	Weak transcription	HSMMtube	muscle
2	chr7:19731600-19746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:19732600-19747000	Weak transcription	Pancreas	Pancrea
4	chr7:19733000-19747400	Weak transcription	Spleen	Spleen
5	chr7:19733800-19747000	Weak transcription	Osteobl	bone
6	chr7:19733800-19747400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr7:19734000-19746600	Weak transcription	Fetal Lung	lung
8	chr7:19734200-19746800	Weak transcription	Psoas Muscle	Psoas
9	chr7:19734400-19747000	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:19734400-19747400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:19734600-19746400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:19734800-19747000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:19734800-19748000	Weak transcription	Lung	lung
14	chr7:19735400-19746400	Weak transcription	HMEC	breast
15	chr7:19735400-19747000	Weak transcription	Right Ventricle	heart
16	chr7:19735400-19747200	Weak transcription	Fetal Heart	heart
17	chr7:19735600-19746800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:19735800-19746800	Weak transcription	Brain Angular Gyrus	brain
19	chr7:19735800-19747000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:19735800-19747000	Weak transcription	Small Intestine	intestine
21	chr7:19735800-19747000	Weak transcription	Thymus	Thymus
22	chr7:19735800-19747800	Weak transcription	Colonic Mucosa	Colon
23	chr7:19736000-19746600	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:19736000-19748000	Weak transcription	Gastric	stomach
25	chr7:19736200-19747600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:19736400-19746600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:19736600-19746800	Weak transcription	NHLF	lung
28	chr7:19736800-19746400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr7:19736800-19746800	Weak transcription	Brain Substantia Nigra	brain
30	chr7:19737400-19747000	Weak transcription	Ovary	ovary
31	chr7:19737800-19746600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr7:19738200-19746400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:19738200-19746600	Weak transcription	NH-A	brain
34	chr7:19738200-19746800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr7:19738200-19747000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr7:19738200-19748000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:19738400-19746800	Weak transcription	Colon Smooth Muscle	Colon
38	chr7:19739400-19746800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:19740000-19748000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:19740200-19746600	Weak transcription	Adipose Nuclei	Adipose
41	chr7:19741600-19746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr7:19741800-19746600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:19741800-19746800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr7:19741800-19746800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:19741800-19747600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr7:19742000-19746600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr7:19742200-19746600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:19742200-19746600	Weak transcription	Brain Anterior Caudate	brain
49	chr7:19742200-19747800	Weak transcription	Placenta	Placenta
50	chr7:19742800-19746400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links