Variant report

Variant	rs4549741
Chromosome Location	chr8:99748557-99748558
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:99738155..99743366-chr8:99746593..99750391,4	MCF-7	breast:
2	chr8:99742630..99744951-chr8:99747576..99749535,2	MCF-7	breast:
3	chr8:99739198..99741801-chr8:99746895..99749270,2	MCF-7	breast:
4	chr8:99748081..99750351-chr8:99836691..99838488,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104375	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10447977	0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes]
rs10755896	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10755897	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10955186	0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs10955187	0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs10955189	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10955190	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11774463	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11778767	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11780292	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11780369	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11780500	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11785245	0.90[JPT][hapmap]
rs12114834	0.82[CHB][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes]
rs12541317	0.85[AMR][1000 genomes]
rs12542069	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12542649	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12542758	0.82[CHB][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12547297	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12549803	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12550012	0.89[CHD][hapmap]
rs12550783	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12675964	0.86[CHD][hapmap]
rs12677183	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs12679268	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12679734	0.95[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs12680195	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12680602	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13257475	0.95[CHB][hapmap]
rs13269932	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13271844	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13275372	0.80[AMR][1000 genomes]
rs13275915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13279438	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1447245	0.91[MEX][hapmap]
rs1476181	0.82[CHB][hapmap];0.87[AMR][1000 genomes]
rs16897076	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap]
rs2442012	0.91[AMR][1000 genomes]
rs2442014	0.91[AMR][1000 genomes]
rs2515214	0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes]
rs2515216	0.89[GIH][hapmap];0.95[TSI][hapmap]
rs2922066	0.95[MEX][hapmap];0.85[TSI][hapmap]
rs2922075	0.86[AMR][1000 genomes]
rs2922078	0.82[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs2922081	0.86[AMR][1000 genomes]
rs2922082	0.86[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs3019293	0.86[AMR][1000 genomes]
rs34114299	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs34281206	0.87[AMR][1000 genomes]
rs34366206	0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs34477118	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34855977	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35536167	0.87[AMR][1000 genomes]
rs35798019	0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35804297	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4131873	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4255105	0.95[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs4279561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4292660	0.83[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4304299	0.91[AMR][1000 genomes]
rs4413739	0.82[CHB][hapmap];0.90[AMR][1000 genomes]
rs4440607	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4509292	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4517094	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4541872	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4562286	0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes]
rs4612309	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4734410	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4735568	0.91[MEX][hapmap];0.90[TSI][hapmap]
rs4735569	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4735570	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4735571	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4735574	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57034072	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58321500	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58679407	0.83[AMR][1000 genomes]
rs62532565	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62532577	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62532587	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62535381	0.80[AMR][1000 genomes]
rs62535382	0.81[AMR][1000 genomes]
rs62535408	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62535410	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62535412	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6651182	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs6988087	1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs6992925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7818010	0.86[CEU][hapmap];0.87[CHB][hapmap]
rs7818828	0.86[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes]
rs7838239	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7845271	0.83[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs9656842	0.90[TSI][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv891220	chr8:99681858-99867419	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv1025685	chr8:99706280-99826236	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv539691	chr8:99706280-99826236	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4549741	NCALD	cis	cerebellum	SCAN
rs4549741	TMEM14C	trans	cerebellum	SCAN
rs4549741	OSR2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99728200-99757200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr8:99738400-99750000	Weak transcription	Fetal Intestine Small	intestine
3	chr8:99738400-99758000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr8:99739600-99757200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:99739600-99776400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr8:99739800-99757800	Weak transcription	NHEK	skin
7	chr8:99739800-99758000	Weak transcription	Ovary	ovary
8	chr8:99740000-99757200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr8:99741600-99794200	Weak transcription	Pancreas	Pancrea
10	chr8:99743200-99763400	Weak transcription	Right Ventricle	heart
11	chr8:99743400-99777200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr8:99744000-99757000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr8:99746600-99789400	Weak transcription	Psoas Muscle	Psoas
14	chr8:99747000-99749600	Enhancers	GM12878-XiMat	blood
15	chr8:99747600-99758000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr8:99747800-99748600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr8:99747800-99763000	Weak transcription	Osteobl	bone
18	chr8:99748000-99758000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:99748000-99759000	Weak transcription	NHDF-Ad	bronchial
20	chr8:99748200-99748600	Enhancers	Liver	Liver
21	chr8:99748400-99748600	Enhancers	A549	lung

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