Variant report

Variant	rs618159
Chromosome Location	chr11:86935783-86935784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11234978	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11824454	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11825467	0.88[AMR][1000 genomes]
rs2847352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34782550	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34806361	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35707386	0.84[EUR][1000 genomes]
rs4578415	1.00[JPT][hapmap]
rs476642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs482944	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485113	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs489073	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs493708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498407	1.00[ASN][1000 genomes]
rs500725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513938	1.00[JPT][hapmap]
rs520718	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529147	0.82[CEU][hapmap]
rs541345	0.82[GIH][hapmap]
rs542279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs548076	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs556724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs567403	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs570898	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs572253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.86[ASN][1000 genomes]
rs578116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587063	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs605658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs61904207	0.88[AMR][1000 genomes]
rs631930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[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]
rs638771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs654152	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs668768	1.00[ASN][1000 genomes]
rs693653	1.00[ASN][1000 genomes]
rs7950416	0.82[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv898059	chr11:86754948-86949369	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1045057	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv541121	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv468777	chr11:86794856-86985581	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv555707	chr11:86794856-86985581	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv898061	chr11:86850483-86944982	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv468778	chr11:86850483-86974576	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv555708	chr11:86850483-86974576	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv898063	chr11:86864277-86944982	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv898064	chr11:86864277-87013438	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv2829956	chr11:86872504-87025059	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv898065	chr11:86891077-86984439	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv898066	chr11:86891077-86989134	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv898067	chr11:86892865-86935783	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv468779	chr11:86928253-87001892	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv555709	chr11:86928253-87001892	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv898068	chr11:86930270-87005969	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
23	nsv898069	chr11:86932603-86984439	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
24	nsv898070	chr11:86932603-86989134	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs618159	PICALM	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86915400-86942000	Weak transcription	HepG2	liver
2	chr11:86929600-86942000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:86933000-86942800	Weak transcription	Primary B cells from cord blood	blood
4	chr11:86934000-86943600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:86934600-86935800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:86934800-86935800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:86935000-86935800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:86935000-86935800	Enhancers	Adipose Nuclei	Adipose
9	chr11:86935000-86935800	Enhancers	NHDF-Ad	bronchial
10	chr11:86935000-86936600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:86935200-86935800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr11:86935400-86939200	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:86935600-86936400	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links