Variant report

Variant	rs2299949
Chromosome Location	chr7:38492347-38492348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12154302	0.88[ASN][1000 genomes]
rs1558617	0.90[ASN][1000 genomes]
rs17171359	0.83[JPT][hapmap]
rs17171367	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17171377	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17171384	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17171387	0.88[JPT][hapmap]
rs1861239	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2893561	0.86[JPT][hapmap]
rs3735089	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3778876	0.93[JPT][hapmap]
rs3778879	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3778882	0.83[JPT][hapmap]
rs3778887	0.83[JPT][hapmap]
rs3807413	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807416	0.88[JPT][hapmap]
rs3807419	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807425	0.87[JPT][hapmap]
rs3823594	1.00[JPT][hapmap]
rs3823598	0.82[JPT][hapmap]
rs3943706	0.93[JPT][hapmap]
rs41279585	0.90[ASN][1000 genomes]
rs6953928	0.82[JPT][hapmap]
rs6956760	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv1020990	chr7:38257707-38503472	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv1031936	chr7:38319437-38503472	Enhancers Active TSS Weak transcription Flanking Active TSS Strong 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	31 gene(s)	inside rSNPs	diseases
9	nsv830965	chr7:38350614-38521047	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv887964	chr7:38457144-38501065	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1825425	chr7:38457144-38507180	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1815666	chr7:38485901-38499850	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38467800-38495600	Weak transcription	Aorta	Aorta
2	chr7:38471800-38498200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:38476000-38501600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:38489800-38492800	Weak transcription	Brain Angular Gyrus	brain
5	chr7:38490800-38492600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr7:38491600-38493000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:38491600-38493200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:38491600-38493400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:38491600-38493600	Enhancers	Fetal Stomach	stomach
10	chr7:38491800-38492800	Enhancers	Rectal Smooth Muscle	rectum
11	chr7:38491800-38493200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:38491800-38493200	Enhancers	NHDF-Ad	bronchial
13	chr7:38492000-38493200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr7:38492000-38493200	Enhancers	Fetal Heart	heart
15	chr7:38492200-38492600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:38492200-38492600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr7:38492200-38492600	Enhancers	HSMMtube	muscle
18	chr7:38492200-38492800	Enhancers	Brain Hippocampus Middle	brain
19	chr7:38492200-38493200	Enhancers	Fetal Muscle Leg	muscle
20	chr7:38492200-38493200	Enhancers	NHLF	lung
21	chr7:38492200-38493400	Enhancers	Fetal Kidney	kidney
22	chr7:38492200-38493400	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links