Variant report

Variant	rs10885650
Chromosome Location	chr10:116856071-116856072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11197095	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11197117	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11197120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11597403	1.00[YRI][hapmap]
rs12357741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12770988	0.86[EUR][1000 genomes]
rs12779941	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2065719	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2218395	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34873028	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv831998	chr10:116847998-116969618	Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10885650	ATRNL1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116851600-116856200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:116851800-116856200	Active TSS	Brain Anterior Caudate	brain
3	chr10:116852000-116856200	Active TSS	Brain Angular Gyrus	brain
4	chr10:116853800-116856200	Active TSS	Brain Germinal Matrix	brain
5	chr10:116854600-116857800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:116854800-116857800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:116854800-116861600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:116854800-116870000	Weak transcription	Aorta	Aorta
9	chr10:116855000-116856200	Enhancers	Fetal Brain Male	brain
10	chr10:116855000-116856400	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:116855000-116856600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr10:116855200-116856600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr10:116855200-116856600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr10:116855600-116856600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr10:116855600-116859000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr10:116855800-116856200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr10:116855800-116856600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr10:116855800-116857000	Weak transcription	Ovary	ovary
19	chr10:116856000-116856200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr10:116856000-116856400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr10:116856000-116856400	Flanking Active TSS	Fetal Brain Female	brain
22	chr10:116856000-116856400	Active TSS	Fetal Kidney	kidney
23	chr10:116856000-116856400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr10:116856000-116856600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links