Variant report

Variant	rs848638
Chromosome Location	chr2:36808350-36808351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10175266	0.88[EUR][1000 genomes]
rs10178965	0.90[EUR][1000 genomes]
rs10180760	0.88[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs10180792	0.83[CEU][hapmap]
rs10189554	0.89[EUR][1000 genomes]
rs10194100	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10197570	0.84[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs10210291	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs10469897	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs10469898	1.00[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs11124519	0.86[EUR][1000 genomes]
rs11686443	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs11691600	0.96[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs11691767	0.87[CEU][hapmap]
rs11693359	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11886145	0.83[ASN][1000 genomes]
rs11899523	0.88[ASN][1000 genomes]
rs12105545	1.00[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs13029475	0.87[EUR][1000 genomes]
rs13385408	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs13398345	0.88[EUR][1000 genomes]
rs13406169	0.92[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs13406184	0.92[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs13410783	0.89[EUR][1000 genomes]
rs14291	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1523786	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1533946	0.92[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1533947	0.87[EUR][1000 genomes]
rs1533948	0.92[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1533949	0.83[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs17019087	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs17488036	0.80[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2022211	0.84[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs2072533	0.90[EUR][1000 genomes]
rs2072534	0.92[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs2072535	1.00[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2075226	0.92[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2110986	0.90[EUR][1000 genomes]
rs2110987	0.89[EUR][1000 genomes]
rs2160403	0.90[EUR][1000 genomes]
rs2160404	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs2276671	0.92[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs34392255	0.88[EUR][1000 genomes]
rs34425257	0.84[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs3770788	0.89[EUR][1000 genomes]
rs3770793	0.83[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs3770796	0.85[ASN][1000 genomes]
rs3770797	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs3770799	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs3770809	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs3770811	0.92[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs3770818	0.92[CHB][hapmap]
rs3821150	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs5003670	0.83[CEU][hapmap]
rs55700228	0.88[EUR][1000 genomes]
rs6728602	0.88[EUR][1000 genomes]
rs7570763	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs848596	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs848597	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs848598	0.93[ASN][1000 genomes]
rs848600	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs848601	0.92[ASN][1000 genomes]
rs848610	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs848611	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs848612	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs848613	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs848614	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs848616	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs848619	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848622	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs848623	0.94[ASN][1000 genomes]
rs848624	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848627	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs848629	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs848630	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848631	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs848635	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs848636	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848639	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848640	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs861919	0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.92[ASN][1000 genomes]
rs9917316	0.89[EUR][1000 genomes]
rs9917318	0.89[EUR][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	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs848638	CRIM1	cis	cerebellum	SCAN
rs848638	FEZ2	cis	Cerebellum	GTEx
rs848638	FEZ2	cis	cerebellum	SCAN
rs848638	FEZ2	cis	parietal	SCAN
rs848638	FEZ2	cis	Whole Blood	GTEx
rs848638	FEZ2	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36751000-36824200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:36773000-36811200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:36790200-36818000	Strong transcription	Fetal Intestine Large	intestine
4	chr2:36790800-36812000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:36791800-36810400	Weak transcription	Right Atrium	heart
6	chr2:36792200-36810400	Weak transcription	Colonic Mucosa	Colon
7	chr2:36792200-36824200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:36792800-36811400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr2:36793200-36811200	Weak transcription	Pancreas	Pancrea
10	chr2:36793200-36816600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:36795800-36809600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:36796000-36818000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:36796800-36818200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:36797000-36814200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:36797600-36808800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:36797800-36813400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:36798000-36809600	Strong transcription	HSMM	muscle
18	chr2:36798000-36818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:36798200-36818000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr2:36798400-36818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:36798800-36811200	Weak transcription	Gastric	stomach
22	chr2:36799200-36812800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:36799200-36817400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:36799200-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:36799200-36818200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:36799200-36819200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:36799200-36822600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:36799400-36812800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:36799800-36818000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:36800200-36810400	Strong transcription	Osteobl	bone
31	chr2:36800200-36814400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr2:36800200-36817600	Strong transcription	Liver	Liver
33	chr2:36800600-36809000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:36800800-36808600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:36801000-36817800	Strong transcription	HUVEC	blood vessel
36	chr2:36801200-36810800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:36801400-36813200	Strong transcription	Fetal Lung	lung
38	chr2:36801600-36818000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:36801600-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:36801800-36811200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:36801800-36812200	Strong transcription	Fetal Thymus	thymus
42	chr2:36801800-36813800	Strong transcription	Fetal Muscle Leg	muscle
43	chr2:36801800-36814600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:36801800-36816200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:36801800-36817200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:36801800-36818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:36802000-36808400	Strong transcription	Fetal Intestine Small	intestine
48	chr2:36802000-36808600	Strong transcription	Fetal Stomach	stomach
49	chr2:36802000-36808800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:36802000-36818000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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