Variant report

Variant	rs4930856
Chromosome Location	chr12:29310161-29310162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10743645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10743647	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10743648	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10743649	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771486	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771489	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771492	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771494	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843343	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11050084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050098	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11050099	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11050104	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050108	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050110	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050112	0.91[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050114	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12310732	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12319200	0.91[CEU][hapmap]
rs12366549	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1496218	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1561131	1.00[JPT][hapmap]
rs1561132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1826800	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1845819	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1908690	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1908691	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2349971	1.00[JPT][hapmap]
rs2349974	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4105125	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4105126	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4105127	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4105128	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4141943	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4141945	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4323913	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4536271	0.86[ASN][1000 genomes]
rs4930857	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930858	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930859	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4931158	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4931162	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4931163	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4931165	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60287933	0.86[ASN][1000 genomes]
rs6487778	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6487783	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71453727	0.88[ASN][1000 genomes]
rs7294355	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7296268	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7297542	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7309041	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs7309881	0.90[CEU][hapmap];0.82[CHB][hapmap]
rs73265795	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7968949	0.91[CEU][hapmap];0.82[CHB][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7974769	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7975191	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7980923	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs924105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs924107	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs924109	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs958478	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4930856	IFLTD1	cis	parietal	SCAN
rs4930856	ERGIC2	cis	parietal	SCAN
rs4930856	RP11-996F15.2	cis	Thyroid	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29303400-29311400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:29303400-29312200	Weak transcription	Spleen	Spleen
3	chr12:29303400-29316600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:29303400-29317000	Weak transcription	Colonic Mucosa	Colon
5	chr12:29303400-29317800	Weak transcription	Fetal Kidney	kidney
6	chr12:29303600-29313400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:29303800-29310200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:29304000-29312600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:29306000-29312400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:29306400-29310400	Weak transcription	Right Atrium	heart
11	chr12:29306400-29313000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:29306400-29313200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:29306600-29310400	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr12:29306600-29310600	Weak transcription	Adipose Nuclei	Adipose
15	chr12:29306600-29312600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:29306600-29312600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:29306600-29313000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:29306600-29324600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:29306800-29310400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:29306800-29313200	Weak transcription	Fetal Thymus	thymus
21	chr12:29306800-29324400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:29308400-29310200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:29308400-29310200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:29308400-29310200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:29308400-29312600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:29308400-29312600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:29308400-29312600	Weak transcription	K562	blood
28	chr12:29308400-29313200	Weak transcription	Brain Anterior Caudate	brain
29	chr12:29308400-29317000	Weak transcription	Fetal Intestine Small	intestine
30	chr12:29308400-29324000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:29308400-29324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:29308600-29310200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr12:29308600-29310400	Weak transcription	Placenta	Placenta
34	chr12:29308600-29311200	Weak transcription	GM12878-XiMat	blood
35	chr12:29308600-29312600	Weak transcription	Small Intestine	intestine
36	chr12:29308800-29317200	Weak transcription	Dnd41	blood
37	chr12:29309000-29310400	Enhancers	Primary hematopoietic stem cells	blood
38	chr12:29309200-29312600	Enhancers	HUVEC	blood vessel
39	chr12:29309400-29311400	Active TSS	Brain Hippocampus Middle	brain
40	chr12:29309400-29314400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:29309600-29310200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr12:29309600-29310200	Enhancers	NH-A	brain
43	chr12:29309600-29311600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr12:29309800-29310200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:29309800-29311000	Enhancers	Primary B cells from cord blood	blood
46	chr12:29309800-29311400	Enhancers	NHDF-Ad	bronchial
47	chr12:29309800-29312000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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