Variant report

Variant	rs7644623
Chromosome Location	chr3:118691801-118691802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10212391	0.88[AFR][1000 genomes]
rs16829165	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829203	0.87[GIH][hapmap]
rs16829250	0.87[GIH][hapmap]
rs2160054	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs41330049	0.87[GIH][hapmap]
rs41523948	0.92[ASW][hapmap];0.87[GIH][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs4611809	0.96[AFR][1000 genomes]
rs6785161	0.84[YRI][hapmap];0.91[AFR][1000 genomes]
rs6795523	0.92[ASW][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes]
rs72966889	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72968610	0.93[AFR][1000 genomes]
rs7629089	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7633584	0.92[ASW][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9817943	0.93[AFR][1000 genomes]
rs9834188	0.84[AFR][1000 genomes]
rs9837571	0.85[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847272	0.80[LWK][hapmap]
rs9854240	0.88[AFR][1000 genomes]
rs9861721	0.92[ASW][hapmap];0.87[GIH][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs9867214	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs9874337	0.92[AFR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877369	chr3:118681771-118824418	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2756586	chr3:118688611-118863998	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118681200-118694000	Enhancers	Brain Substantia Nigra	brain
2	chr3:118681800-118692800	Enhancers	Brain Anterior Caudate	brain
3	chr3:118683400-118696200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:118684800-118694000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:118688800-118706000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:118689000-118703600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:118690800-118692400	Enhancers	Brain Germinal Matrix	brain
8	chr3:118691000-118692200	Enhancers	Brain Angular Gyrus	brain
9	chr3:118691000-118692800	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr3:118691200-118692400	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:118691200-118692600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:118691200-118693400	Enhancers	Brain Hippocampus Middle	brain
13	chr3:118691200-118693800	Enhancers	Brain Cingulate Gyrus	brain
14	chr3:118691400-118692200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:118691400-118692400	Enhancers	Colon Smooth Muscle	Colon
16	chr3:118691400-118692400	Enhancers	Fetal Heart	heart
17	chr3:118691600-118692200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:118691600-118692200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:118691800-118692000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:118691800-118692000	Enhancers	Stomach Smooth Muscle	stomach
21	chr3:118691800-118692200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:118691800-118692200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr3:118691800-118692400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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