Variant report

Variant	rs7672997
Chromosome Location	chr4:54053351-54053352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10027975	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11133248	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11721940	0.89[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs11724781	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11725172	0.80[MEX][hapmap]
rs11942132	0.82[EUR][1000 genomes]
rs13146499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17654608	0.91[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap]
rs2412401	0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2412403	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2412404	0.89[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs28640919	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34690074	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4394057	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4557334	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4571396	1.00[YRI][hapmap]
rs4588514	0.89[CEU][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs4864737	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6554071	0.89[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.86[EUR][1000 genomes]
rs6554073	0.81[EUR][1000 genomes]
rs6554074	0.82[EUR][1000 genomes]
rs6554075	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6554078	0.82[EUR][1000 genomes]
rs6554093	0.80[MEX][hapmap]
rs6554098	0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6820250	0.84[AMR][1000 genomes]
rs6821328	0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs6822933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827392	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6834382	0.81[ASW][hapmap]
rs751266	0.91[ASW][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs7673864	0.80[EUR][1000 genomes]
rs7675987	0.81[ASW][hapmap]
rs7687452	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7672997	KIAA1211	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54038800-54054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:54043200-54077000	Weak transcription	Primary T cells from cord blood	blood
3	chr4:54048000-54086000	Weak transcription	GM12878-XiMat	blood
4	chr4:54049800-54053600	Weak transcription	NHLF	lung
5	chr4:54050200-54061800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:54050400-54062400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:54050800-54053600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:54051000-54073000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:54052000-54053400	Enhancers	Fetal Lung	lung
10	chr4:54052000-54054200	Enhancers	Liver	Liver
11	chr4:54052000-54054400	Enhancers	Fetal Kidney	kidney
12	chr4:54052000-54054400	Enhancers	Osteobl	bone
13	chr4:54052000-54055400	Enhancers	Fetal Intestine Large	intestine
14	chr4:54052000-54055800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:54052000-54056600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:54052200-54054400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:54052200-54054400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr4:54052200-54054400	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr4:54052200-54054600	Enhancers	K562	blood
20	chr4:54052200-54055800	Enhancers	HepG2	liver
21	chr4:54052200-54056600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:54052200-54056600	Enhancers	NHDF-Ad	bronchial
23	chr4:54052400-54053600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:54052400-54054400	Weak transcription	Ovary	ovary
25	chr4:54052400-54056000	Enhancers	NH-A	brain
26	chr4:54052400-54065800	Weak transcription	Aorta	Aorta
27	chr4:54052600-54054200	Weak transcription	Fetal Intestine Small	intestine
28	chr4:54052800-54053600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:54052800-54054200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:54052800-54054400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:54052800-54054400	Weak transcription	Fetal Stomach	stomach
32	chr4:54052800-54056600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:54053000-54053800	Weak transcription	HSMM	muscle
34	chr4:54053000-54054000	Weak transcription	HSMMtube	muscle
35	chr4:54053000-54054400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:54053000-54093000	Weak transcription	Primary B cells from cord blood	blood
37	chr4:54053200-54054200	Weak transcription	Brain Substantia Nigra	brain
38	chr4:54053200-54058000	Weak transcription	Small Intestine	intestine

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