Variant report

Variant	rs834584
Chromosome Location	chr3:42978842-42978843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42976404..42980028-chr3:42981618..42984060,3	K562	blood:
2	chr3:42977585..42980028-chr3:42981618..42983637,2	K562	blood:

Variant related genes	Relation type
ENSG00000240747	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10470680	0.83[EUR][1000 genomes]
rs11129987	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346414	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1346415	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1403525	0.82[TSI][hapmap]
rs17074894	0.82[EUR][1000 genomes]
rs2288371	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2288372	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2288373	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2372270	0.80[EUR][1000 genomes]
rs28378297	0.80[EUR][1000 genomes]
rs339682	1.00[CHD][hapmap]
rs339683	1.00[CHD][hapmap]
rs3915020	0.82[EUR][1000 genomes]
rs526511	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs542394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs551658	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59789275	0.87[ASN][1000 genomes]
rs60046829	0.87[ASN][1000 genomes]
rs60607395	0.87[ASN][1000 genomes]
rs60616619	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61004728	0.83[EUR][1000 genomes]
rs61102947	0.87[ASN][1000 genomes]
rs615462	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs619660	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62249006	0.83[EUR][1000 genomes]
rs62249007	0.83[EUR][1000 genomes]
rs62249008	0.82[EUR][1000 genomes]
rs62249009	0.83[EUR][1000 genomes]
rs62249011	0.83[EUR][1000 genomes]
rs62249013	0.82[EUR][1000 genomes]
rs638602	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs649682	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6763762	0.83[EUR][1000 genomes]
rs6773223	0.82[EUR][1000 genomes]
rs6775999	0.83[EUR][1000 genomes]
rs6778645	0.95[ASN][1000 genomes]
rs6779194	0.87[ASN][1000 genomes]
rs6798412	1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs6798520	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6865	1.00[CHD][hapmap]
rs704895	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs704899	1.00[CEU][hapmap]
rs735320	1.00[CHD][hapmap]
rs7617715	0.80[EUR][1000 genomes]
rs7621158	0.87[ASN][1000 genomes]
rs7625959	1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs7641452	1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap]
rs7644923	0.83[EUR][1000 genomes]
rs834183	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs834325	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs834579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834699	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9311330	0.80[EUR][1000 genomes]
rs9311331	0.83[EUR][1000 genomes]
rs9808932	0.82[EUR][1000 genomes]
rs9832875	0.81[GIH][hapmap]
rs9833284	0.83[EUR][1000 genomes]
rs9852930	0.82[EUR][1000 genomes]
rs9858270	0.82[EUR][1000 genomes]
rs9874514	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs834584	HIGD1A	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42962400-42980400	Weak transcription	Placenta	Placenta
2	chr3:42977800-42986600	Weak transcription	Fetal Brain Male	brain
3	chr3:42978200-42983400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:42978200-42983400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:42978200-42984400	Weak transcription	Aorta	Aorta
6	chr3:42978200-42984600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:42978200-42984600	Weak transcription	Psoas Muscle	Psoas
8	chr3:42978200-42984800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:42978200-42984800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:42978400-42980400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:42978400-42981200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:42978400-42982600	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:42978400-42982600	Weak transcription	Fetal Intestine Large	intestine
14	chr3:42978400-42982600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:42978400-42984600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:42978400-42984800	Weak transcription	Brain Substantia Nigra	brain
17	chr3:42978400-42985000	Weak transcription	Adipose Nuclei	Adipose
18	chr3:42978400-42985200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:42978400-42985400	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:42978400-42986200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:42978400-42989000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:42978400-42990600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:42978400-42994400	Weak transcription	Fetal Stomach	stomach
24	chr3:42978400-42995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:42978400-43003000	Weak transcription	Fetal Intestine Small	intestine
26	chr3:42978400-43015400	Weak transcription	Pancreas	Pancrea
27	chr3:42978600-42980600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:42978600-42982600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:42978600-42984800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:42978600-42987800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:42978600-42989000	Weak transcription	Fetal Kidney	kidney
32	chr3:42978600-42991000	Weak transcription	Brain Anterior Caudate	brain
33	chr3:42978600-43003000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:42978600-43020400	Weak transcription	Ovary	ovary
35	chr3:42978800-42979000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links