Variant report

Variant	rs10513019
Chromosome Location	chr5:52944428-52944429
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52943856..52946285-chr5:52969298..52971904,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11738542	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11740228	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11740800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11741008	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749849	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16881514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16881524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16881561	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847471	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2087618	0.87[AFR][1000 genomes]
rs2124948	0.81[LWK][hapmap]
rs28855127	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3958630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4147735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147742	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4549481	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640749	0.89[ASN][1000 genomes]
rs55828101	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6872395	0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs6892641	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72750138	0.82[ASN][1000 genomes]
rs72750151	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751832	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751833	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751838	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751849	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72753647	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753650	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753658	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753680	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72755395	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72757304	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72757372	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72757390	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7716949	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv881237	chr5:52885100-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv880426	chr5:52885100-52953048	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv880762	chr5:52894276-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10513019	NDUFS4	cis	parietal	SCAN
rs10513019	CDC20B	cis	parietal	SCAN
rs10513019	ARL15	cis	cerebellum	SCAN
rs10513019	HSPB3	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52904400-52966600	Weak transcription	Osteobl	bone
2	chr5:52920800-52978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:52921600-52963400	Weak transcription	A549	lung
4	chr5:52925600-52961200	Weak transcription	Esophagus	oesophagus
5	chr5:52925800-52952000	Weak transcription	Colonic Mucosa	Colon
6	chr5:52926600-52948800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:52926800-52963600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:52927400-52945000	Weak transcription	Fetal Brain Female	brain
9	chr5:52927400-52961000	Weak transcription	Placenta	Placenta
10	chr5:52927800-52948600	Weak transcription	Pancreas	Pancrea
11	chr5:52927800-52961200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:52927800-52961200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr5:52927800-52961200	Weak transcription	Thymus	Thymus
14	chr5:52928000-52945000	Weak transcription	Fetal Intestine Small	intestine
15	chr5:52928000-52946000	Weak transcription	Gastric	stomach
16	chr5:52928000-52962200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:52929000-52981800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:52929200-52947600	Weak transcription	Right Ventricle	heart
19	chr5:52929400-52964600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:52931000-52944600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:52933200-52951600	Weak transcription	Aorta	Aorta
22	chr5:52935200-52978000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:52936600-52948400	Weak transcription	Lung	lung
24	chr5:52937200-52963600	Weak transcription	NHLF	lung
25	chr5:52938200-52945200	Weak transcription	Adipose Nuclei	Adipose
26	chr5:52938200-52954800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:52938200-52970200	Weak transcription	NH-A	brain
28	chr5:52938400-52952400	Weak transcription	Small Intestine	intestine
29	chr5:52938400-52961000	Weak transcription	Fetal Stomach	stomach
30	chr5:52938400-52967600	Weak transcription	Fetal Kidney	kidney
31	chr5:52938600-52944600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:52938600-52944600	Weak transcription	HSMM	muscle
33	chr5:52938600-52945000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr5:52938600-52946600	Weak transcription	HUVEC	blood vessel
35	chr5:52938600-52971000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr5:52938800-52945200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:52939600-52945200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:52939600-52945200	Weak transcription	Brain Angular Gyrus	brain
39	chr5:52939600-52960600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:52939800-52945000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr5:52939800-52945200	Weak transcription	NHEK	skin
42	chr5:52939800-52946000	Weak transcription	Colon Smooth Muscle	Colon
43	chr5:52939800-52959600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:52940000-52982000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:52941200-52963400	Weak transcription	Hela-S3	cervix
46	chr5:52941400-52980200	Weak transcription	HepG2	liver
47	chr5:52941400-52985200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr5:52941600-52945200	Weak transcription	HSMMtube	muscle
49	chr5:52941600-52945600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr5:52941600-52945600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links