Variant report

Variant	rs12138544
Chromosome Location	chr1:62743398-62743399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr1:62743221-62743414	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
KANK4	TF binding region

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10157938	0.88[JPT][hapmap]
rs10465842	0.90[JPT][hapmap]
rs10493318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889318	0.90[JPT][hapmap]
rs11207955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207956	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031172	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031176	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038843	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12043263	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12123763	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127630	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555832	0.81[ASN][1000 genomes]
rs17855078	0.90[ASN][1000 genomes]
rs1886834	0.90[JPT][hapmap]
rs1925827	0.86[JPT][hapmap]
rs2666509	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs2765266	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2765268	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2765269	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs34477066	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850629	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3850632	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs3861936	1.00[JPT][hapmap]
rs4915606	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs4915607	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs6675508	0.90[JPT][hapmap]
rs6680736	0.83[EUR][1000 genomes]
rs6691591	0.83[EUR][1000 genomes]
rs881548	0.90[JPT][hapmap]
rs9803815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9803854	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9804022	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:62734200-62750800	Weak transcription	Gastric	stomach
3	chr1:62737800-62744400	Weak transcription	Fetal Intestine Large	intestine
4	chr1:62738000-62749000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:62738200-62746400	Weak transcription	Fetal Kidney	kidney
6	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:62739600-62744200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:62740200-62746400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:62740400-62744600	Weak transcription	Fetal Thymus	thymus
10	chr1:62740400-62745400	Weak transcription	Fetal Lung	lung
11	chr1:62740400-62746600	Weak transcription	Pancreas	Pancrea
12	chr1:62740600-62744400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:62740600-62744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:62740600-62744600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:62741000-62745000	Weak transcription	HepG2	liver
16	chr1:62741200-62744400	Weak transcription	Fetal Heart	heart
17	chr1:62741800-62744600	Weak transcription	Placenta	Placenta
18	chr1:62742600-62743400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:62742600-62743600	ZNF genes & repeats	Adipose Nuclei	Adipose
20	chr1:62742800-62743400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr1:62743000-62743400	ZNF genes & repeats	Fetal Intestine Small	intestine
22	chr1:62743000-62743800	ZNF genes & repeats	Fetal Muscle Leg	muscle
23	chr1:62743200-62743400	ZNF genes & repeats	Fetal Stomach	stomach
24	chr1:62743200-62744000	ZNF genes & repeats	Liver	Liver
25	chr1:62743200-62746800	Weak transcription	HMEC	breast
26	chr1:62743200-62747800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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