Variant report

Variant	rs1523125
Chromosome Location	chr3:43115161-43115162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1072822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1125065	0.84[GIH][hapmap];1.00[MEX][hapmap]
rs12233614	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12485530	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485578	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12487785	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497427	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497602	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1523126	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1566422	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17391761	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17470089	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1815070	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1949583	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1949584	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs488069	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55764298	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55819365	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55945909	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55954171	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604033	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796161	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73074962	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7624799	1.00[LWK][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	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
3	nsv979767	chr3:43114716-43117256	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1523125	CCDC13	cis	parietal	SCAN
rs1523125	ABHD5	cis	parietal	SCAN

Chromatin state (count:22 , 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	chr3:43096200-43121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:43100200-43120200	Weak transcription	Brain Angular Gyrus	brain
5	chr3:43101600-43121000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:43102000-43121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:43102800-43118800	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:43103000-43120000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:43103200-43120600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:43104800-43120800	Weak transcription	Gastric	stomach
11	chr3:43105000-43118800	Weak transcription	Thymus	Thymus
12	chr3:43105000-43119600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:43106000-43115600	Weak transcription	Ovary	ovary
14	chr3:43106400-43119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:43106400-43120400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:43112200-43121200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:43112800-43120600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:43113000-43120800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:43114800-43115200	Enhancers	Brain Anterior Caudate	brain
20	chr3:43114800-43115800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:43114800-43118400	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:43115000-43120400	Weak transcription	Fetal Intestine Small	intestine

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