Variant report

Variant	rs7935948
Chromosome Location	chr11:73219118-73219119
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	CEBPB	chr11:73218941-73219241	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73216954..73219144-chr11:73356797..73358531,2	K562	blood:

Variant related genes	Relation type
ENSG00000256148	TF binding region
ENSG00000021300	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1002126	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1002127	1.00[CEU][hapmap]
rs10501411	0.89[CEU][hapmap]
rs11235738	1.00[JPT][hapmap]
rs11235745	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11235746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11235759	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11235770	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11235775	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11235809	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820929	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11821094	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11823913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11823923	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11824614	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11826896	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11826909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11828904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12269884	1.00[JPT][hapmap]
rs12274589	1.00[JPT][hapmap]
rs12275766	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12276892	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12277924	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282282	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12282790	1.00[JPT][hapmap]
rs12285885	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12290623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs12290701	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12290835	1.00[JPT][hapmap]
rs17132115	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244596	1.00[CEU][hapmap]
rs17244602	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17244616	1.00[CEU][hapmap]
rs17310361	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17310374	1.00[CEU][hapmap]
rs17851510	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap]
rs1894076	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1938777	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs2027760	0.89[CEU][hapmap]
rs2027761	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs2027763	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2298469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs2298807	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3741149	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3825005	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3933402	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs56857598	0.82[EUR][1000 genomes]
rs57673166	0.82[EUR][1000 genomes]
rs58573166	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59806295	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60860405	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61516411	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6592521	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7101831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7102197	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7105681	0.89[CEU][hapmap]
rs7110369	0.89[CEU][hapmap]
rs7113420	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7114009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes]
rs7114376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115055	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7118982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7122825	0.89[CEU][hapmap]
rs7123298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7123985	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs7125978	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7129990	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs7131383	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7131397	1.00[JPT][hapmap]
rs724111	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs725103	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7342205	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs73544783	0.82[EUR][1000 genomes]
rs7925226	1.00[CEU][hapmap]
rs7927344	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930152	0.82[EUR][1000 genomes]
rs7930454	0.89[CEU][hapmap]
rs7930880	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7931767	0.82[EUR][1000 genomes]
rs7933355	0.82[EUR][1000 genomes]
rs7934218	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938391	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941359	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7944099	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7944346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945825	1.00[CEU][hapmap]
rs7951072	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7952686	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs876480	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs880317	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs947837	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9888218	1.00[JPT][hapmap]

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	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv508641	chr11:73149281-73235528	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv520130	chr11:73183598-73223776	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv1048171	chr11:73210060-73271831	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7935948	ARHGEF17	cis	multi-tissue	Pritchard
rs7935948	CCND1	cis	cerebellum	SCAN
rs7935948	P2RY2	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73141800-73231600	Weak transcription	Thymus	Thymus
2	chr11:73163800-73225600	Weak transcription	Fetal Stomach	stomach
3	chr11:73182000-73230000	Weak transcription	Dnd41	blood
4	chr11:73202400-73240000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:73205000-73239600	Weak transcription	Primary B cells from cord blood	blood
6	chr11:73205200-73219600	Weak transcription	Brain Germinal Matrix	brain
7	chr11:73205600-73236400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:73205800-73241400	Weak transcription	Pancreas	Pancrea
9	chr11:73206000-73222000	Weak transcription	Left Ventricle	heart
10	chr11:73206200-73224600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:73206200-73232600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:73207600-73225600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr11:73209400-73221600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:73209800-73219600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:73210200-73231400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:73212600-73220200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:73215600-73232200	Weak transcription	A549	lung
18	chr11:73216600-73223000	Weak transcription	Fetal Brain Male	brain
19	chr11:73217400-73221800	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:73217400-73221800	Weak transcription	Brain Substantia Nigra	brain
21	chr11:73217400-73231400	Weak transcription	Primary T cells from cord blood	blood
22	chr11:73218000-73219800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:73218400-73219600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:73218600-73219600	Enhancers	NHDF-Ad	bronchial
25	chr11:73218600-73232600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:73218800-73220000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:73218800-73220200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:73218800-73221600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:73219000-73231400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:73219000-73232200	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links