Variant report

Variant	rs12509636
Chromosome Location	chr4:106010433-106010434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10856976	1.00[JPT][hapmap]
rs168989	0.86[CHB][hapmap]
rs17429675	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17429682	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17429745	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17501550	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1844655	0.86[CHB][hapmap]
rs195149	0.86[CHB][hapmap]
rs2214409	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2301718	0.83[GIH][hapmap]
rs4698931	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4699151	0.86[CHB][hapmap]
rs4699152	0.82[CHD][hapmap]
rs4699153	1.00[JPT][hapmap]
rs56883672	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62331120	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62331124	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72617743	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830024	chr4:105884350-106037816	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106008400-106011200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:106008400-106011200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr4:106009800-106010600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:106009800-106010600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr4:106009800-106013400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:106010000-106014000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:106010200-106010600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:106010200-106010600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr4:106010200-106010800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:106010200-106013400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:106010200-106013400	Weak transcription	HMEC	breast
12	chr4:106010200-106013400	Weak transcription	NH-A	brain
13	chr4:106010200-106013800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:106010400-106010800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:106010400-106013400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:106010400-106013400	Weak transcription	NHDF-Ad	bronchial
17	chr4:106010400-106013400	Weak transcription	Osteobl	bone
18	chr4:106010400-106014000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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