Variant report

Variant	rs6814979
Chromosome Location	chr4:159056950-159056951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10000610	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10003459	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs10013448	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10027000	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs10049927	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs10517684	0.80[JPT][hapmap]
rs10857307	0.80[JPT][hapmap]
rs10857308	0.80[JPT][hapmap]
rs12511578	0.80[JPT][hapmap]
rs12512643	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13126694	0.81[CHB][hapmap];0.91[MEX][hapmap]
rs17036918	0.80[JPT][hapmap]
rs17036921	0.80[JPT][hapmap]
rs2245735	0.93[JPT][hapmap]
rs2346782	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4077776	0.92[CEU][hapmap];0.94[CHB][hapmap]
rs4129400	0.80[JPT][hapmap]
rs4388135	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs4460050	0.80[JPT][hapmap]
rs4574459	0.89[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs4631100	0.89[CEU][hapmap];0.88[CHB][hapmap]
rs4691449	0.80[JPT][hapmap]
rs4691454	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4691460	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs6536298	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs6830475	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs6833295	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6843728	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs7384	0.93[JPT][hapmap]
rs7657303	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs7692254	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs9968557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]

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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6814979	DKFZp434L142	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159042600-159060200	Weak transcription	Brain Substantia Nigra	brain
2	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:159044800-159071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:159044800-159073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:159045200-159058600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr4:159045200-159059400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr4:159047000-159080200	Weak transcription	Right Ventricle	heart
8	chr4:159047200-159058600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:159049200-159070000	Weak transcription	Placenta	Placenta
10	chr4:159051000-159061000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:159051800-159070600	Weak transcription	Fetal Intestine Large	intestine
12	chr4:159051800-159073000	Weak transcription	Fetal Stomach	stomach
13	chr4:159051800-159080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:159052000-159071400	Weak transcription	Adipose Nuclei	Adipose
15	chr4:159052200-159071400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:159052200-159072800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:159052400-159060200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:159052600-159060400	Weak transcription	Ovary	ovary
19	chr4:159052600-159071200	Weak transcription	Fetal Intestine Small	intestine
20	chr4:159052600-159071400	Weak transcription	HSMMtube	muscle
21	chr4:159052600-159080200	Weak transcription	Left Ventricle	heart
22	chr4:159052800-159060200	Weak transcription	HMEC	breast
23	chr4:159053800-159060600	Weak transcription	Brain Anterior Caudate	brain
24	chr4:159054000-159059000	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:159054200-159058000	Weak transcription	HUVEC	blood vessel
26	chr4:159054200-159059200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:159054200-159063600	Weak transcription	HepG2	liver
28	chr4:159054600-159059400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:159055600-159058200	Strong transcription	HSMM	muscle
30	chr4:159055600-159061800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:159055600-159076200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:159056200-159058200	Weak transcription	Fetal Heart	heart
33	chr4:159056200-159058400	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:159056800-159058600	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links