Variant report

Variant	rs1481279
Chromosome Location	chr4:103977938-103977939
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10006474	0.84[GIH][hapmap];0.85[JPT][hapmap]
rs10516495	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs10516496	0.91[GIH][hapmap];0.86[JPT][hapmap]
rs11946020	0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs13113099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13149311	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150953	0.93[GIH][hapmap];0.86[JPT][hapmap]
rs34475639	0.91[GIH][hapmap];0.86[JPT][hapmap]
rs4699048	0.82[JPT][hapmap]
rs6816370	0.86[JPT][hapmap]
rs6843738	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs7665026	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs7665217	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7674212	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap]
rs7675837	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7691873	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
3	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1481279	CISD2	cis	cerebellum	SCAN
rs1481279	KRT8P46	cis	lung	GTEx
rs1481279	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103941400-103989400	Weak transcription	NH-A	brain
2	chr4:103941400-103996600	Weak transcription	Lung	lung
3	chr4:103941600-103989000	Weak transcription	HMEC	breast
4	chr4:103941800-103994600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:103942000-103994400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:103942000-103995200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:103947800-103996000	Weak transcription	Brain Angular Gyrus	brain
8	chr4:103952400-103994600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr4:103952800-103996600	Weak transcription	Fetal Stomach	stomach
10	chr4:103954000-103996200	Weak transcription	Gastric	stomach
11	chr4:103957600-103995400	Weak transcription	Ovary	ovary
12	chr4:103960800-103991200	Weak transcription	Psoas Muscle	Psoas
13	chr4:103962800-103995000	Weak transcription	Small Intestine	intestine
14	chr4:103963600-103996600	Weak transcription	Pancreas	Pancrea
15	chr4:103965800-103994800	Weak transcription	K562	blood
16	chr4:103966000-103987000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:103966000-103987000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:103966000-103995400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:103966000-103996600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:103966600-103996600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:103968400-103996200	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:103970000-103989000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:103970200-103983000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:103970200-103995000	Weak transcription	Fetal Brain Male	brain
25	chr4:103970200-103996600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:103970400-103984000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr4:103970400-103987000	Weak transcription	HSMM	muscle
28	chr4:103970400-103996600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:103970600-103996000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:103970600-103996200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:103970800-103982000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:103970800-103982600	Weak transcription	Fetal Brain Female	brain
33	chr4:103970800-103987200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:103970800-103995000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr4:103970800-103995400	Weak transcription	Primary B cells from cord blood	blood
36	chr4:103970800-103996000	Weak transcription	Primary T cells from cord blood	blood
37	chr4:103970800-103996600	Weak transcription	Adipose Nuclei	Adipose
38	chr4:103971000-103981400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:103971000-103985200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:103971000-103987000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:103971000-103996000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:103971000-103996200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:103971200-103987200	Weak transcription	Brain Germinal Matrix	brain
44	chr4:103971200-103995400	Weak transcription	Brain Anterior Caudate	brain
45	chr4:103971200-103996200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:103971200-103996200	Weak transcription	Left Ventricle	heart
47	chr4:103971400-103984800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr4:103971400-103986000	Weak transcription	HUVEC	blood vessel
49	chr4:103971400-103995200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr4:103971400-103996200	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links