Variant report

Variant	rs513875
Chromosome Location	chr3:43104383-43104384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11707725	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11716441	0.82[EUR][1000 genomes]
rs11719573	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12639294	0.93[ASW][hapmap];0.80[MKK][hapmap];0.95[YRI][hapmap]
rs17075162	0.82[ASN][1000 genomes]
rs1949585	0.95[YRI][hapmap]
rs737351	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7619872	0.80[ASN][1000 genomes]
rs834176	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs513875	CCDC13	cis	parietal	SCAN
rs513875	C3orf39	cis	cerebellum	SCAN
rs513875	XIRP1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43092800-43117800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:43093400-43120200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:43094400-43114800	Weak transcription	Brain Anterior Caudate	brain
4	chr3:43095000-43114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:43095800-43104400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:43096200-43121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:43097200-43104600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:43100200-43120200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:43101000-43105000	Enhancers	Fetal Thymus	thymus
10	chr3:43101600-43121000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:43101800-43105000	ZNF genes & repeats	Fetal Stomach	stomach
12	chr3:43102000-43121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:43102800-43118800	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:43103000-43120000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:43103200-43104400	Enhancers	Right Atrium	heart
16	chr3:43103200-43120600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:43103400-43105000	Strong transcription	Stomach Smooth Muscle	stomach
18	chr3:43103400-43105400	Strong transcription	Liver	Liver
19	chr3:43103600-43104800	Enhancers	K562	blood
20	chr3:43103800-43104400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:43103800-43104800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:43103800-43105000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:43104000-43104400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:43104000-43105000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:43104000-43105000	Genic enhancers	Placenta	Placenta
26	chr3:43104200-43104400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:43104200-43104400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:43104200-43104400	Enhancers	Fetal Muscle Trunk	muscle
29	chr3:43104200-43104400	Genic enhancers	Fetal Muscle Leg	muscle
30	chr3:43104200-43104600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:43104200-43104600	Genic enhancers	Thymus	Thymus
32	chr3:43104200-43104800	Strong transcription	Gastric	stomach
33	chr3:43104200-43105000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:43104200-43105400	Enhancers	Dnd41	blood
35	chr3:43104200-43106000	Strong transcription	Ovary	ovary
36	chr3:43104200-43106400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links