Variant report

Variant	rs1179494
Chromosome Location	chr2:36809496-36809497
allele	C/G
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	ZNF384	chr2:36809479-36809660	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36809008..36811077-chr2:36815075..36817974,3	MCF-7	breast:
2	chr2:36809435..36813840-chr2:36817141..36820574,5	K562	blood:

Variant related genes	Relation type
FEZ2	TF binding region
ENSG00000256845	Chromatin interaction
ENSG00000171055	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10179862	0.87[CHB][hapmap]
rs10180760	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs10197570	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs10210291	0.91[CHB][hapmap]
rs10469897	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10469898	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs11899523	0.90[EUR][1000 genomes]
rs12712508	0.90[CHB][hapmap]
rs13000354	0.80[EUR][1000 genomes]
rs1533946	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs1533948	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs17019087	0.86[CHB][hapmap]
rs2022211	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2072533	0.93[ASN][1000 genomes]
rs2072534	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2072535	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2075226	0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2110986	0.93[ASN][1000 genomes]
rs2160404	0.90[CHB][hapmap]
rs2276671	0.86[TSI][hapmap]
rs34392255	0.93[ASN][1000 genomes]
rs34425257	0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3770788	0.93[ASN][1000 genomes]
rs3770796	0.90[EUR][1000 genomes]
rs3770797	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs3770809	0.86[CHB][hapmap]
rs3770811	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs3770818	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs3821150	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs55700228	0.93[ASN][1000 genomes]
rs57670037	0.82[ASN][1000 genomes]
rs6728602	0.90[ASN][1000 genomes]
rs7570763	0.96[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs848603	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs848605	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs848606	0.86[CHB][hapmap]
rs848607	0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[TSI][hapmap]
rs848617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848642	0.84[CEU][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs848643	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs981355	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs9917316	0.89[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1179494	CRIM1	cis	cerebellum	SCAN
rs1179494	FEZ2	cis	multi-tissue	Pritchard
rs1179494	FEZ2	cis	cerebellum	SCAN
rs1179494	FEZ2	cis	lymphoblastoid	seeQTL

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	chr2:36797800-36813400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:36798000-36809600	Strong transcription	HSMM	muscle
17	chr2:36798000-36818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:36798200-36818000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:36798400-36818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:36798800-36811200	Weak transcription	Gastric	stomach
21	chr2:36799200-36812800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:36799200-36817400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:36799200-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:36799200-36818200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:36799200-36819200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:36799200-36822600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:36799400-36812800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:36799800-36818000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:36800200-36810400	Strong transcription	Osteobl	bone
30	chr2:36800200-36814400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr2:36800200-36817600	Strong transcription	Liver	Liver
32	chr2:36801000-36817800	Strong transcription	HUVEC	blood vessel
33	chr2:36801200-36810800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:36801400-36813200	Strong transcription	Fetal Lung	lung
35	chr2:36801600-36818000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:36801600-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:36801800-36811200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:36801800-36812200	Strong transcription	Fetal Thymus	thymus
39	chr2:36801800-36813800	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:36801800-36814600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:36801800-36816200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:36801800-36817200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:36801800-36818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:36802000-36818000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:36802000-36823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:36802400-36815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:36802800-36811400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:36802800-36812400	Strong transcription	NH-A	brain
49	chr2:36803000-36810800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:36803200-36813400	Strong transcription	Primary T cells fromperipheralblood	blood

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