Variant report

Variant	rs10880087
Chromosome Location	chr12:41905419-41905420
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:41903994..41905628-chr12:41905672..41908634,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10459287	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10506188	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10506193	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10748302	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10785269	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10880081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880086	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880089	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880091	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880093	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880095	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10880096	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880097	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11180936	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180943	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180961	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180979	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11180981	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11180984	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11180988	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11180989	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11180994	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12229610	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12230775	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12372586	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1458153	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs169564	0.85[JPT][hapmap]
rs17579291	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902908	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2054211	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2608709	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2730812	1.00[JPT][hapmap]
rs2730831	0.85[JPT][hapmap]
rs285551	0.85[JPT][hapmap]
rs285559	1.00[JPT][hapmap]
rs285583	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs285586	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs285587	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs285588	1.00[JPT][hapmap]
rs285596	1.00[JPT][hapmap]
rs285597	0.85[JPT][hapmap]
rs287087	1.00[JPT][hapmap]
rs3110189	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4768355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725527	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73130674	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv826349	chr12:41878846-41911495	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41898600-41915400	Weak transcription	Aorta	Aorta
2	chr12:41899000-41906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:41902000-41909400	Enhancers	Brain Germinal Matrix	brain
4	chr12:41902200-41908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:41902400-41907400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:41902400-41907800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:41902400-41915000	Weak transcription	Brain Anterior Caudate	brain
8	chr12:41902600-41907600	Weak transcription	Brain Substantia Nigra	brain
9	chr12:41902600-41907800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:41902600-41907800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:41903800-41907400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:41904400-41908800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:41904600-41905600	Enhancers	Brain Hippocampus Middle	brain
14	chr12:41904600-41915600	Weak transcription	Fetal Kidney	kidney
15	chr12:41904800-41907400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:41905000-41905600	Enhancers	Fetal Brain Female	brain
17	chr12:41905000-41908000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:41905200-41905800	Enhancers	Colon Smooth Muscle	Colon
19	chr12:41905200-41906400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:41905200-41916400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:41905400-41905800	Enhancers	Brain Cingulate Gyrus	brain
22	chr12:41905400-41907600	Weak transcription	Fetal Heart	heart

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