Variant report

Variant	rs12617686
Chromosome Location	chr2:153351829-153351830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10166703	0.81[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs10173398	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10193625	0.81[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10195380	0.94[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10432494	0.93[ASN][1000 genomes]
rs11892232	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11892859	0.95[ASN][1000 genomes]
rs11893683	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614608	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623070	0.81[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2068886	0.86[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2346204	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2881336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146259	0.85[CEU][hapmap]
rs4471845	0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4613221	0.96[ASN][1000 genomes]
rs4664585	0.85[MKK][hapmap]
rs6434078	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6736639	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737006	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7425826	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7590079	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7606592	0.85[CEU][hapmap]
rs9288103	0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12617686	PRPF40A	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153334400-153353800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:153338600-153353400	Weak transcription	NHEK	skin
3	chr2:153340600-153354200	Weak transcription	Small Intestine	intestine
4	chr2:153342600-153355800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:153343000-153360600	Enhancers	Brain Anterior Caudate	brain
6	chr2:153346200-153352800	Weak transcription	GM12878-XiMat	blood
7	chr2:153347600-153354200	Weak transcription	Pancreas	Pancrea
8	chr2:153347800-153354400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:153348000-153352000	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:153348000-153352800	Weak transcription	Fetal Brain Male	brain
11	chr2:153348000-153354200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:153348200-153352600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:153348600-153354200	Weak transcription	Fetal Intestine Large	intestine
14	chr2:153348600-153354200	Weak transcription	Placenta	Placenta
15	chr2:153348600-153357200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:153348800-153354200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:153348800-153370200	Weak transcription	Aorta	Aorta
18	chr2:153350000-153352000	Enhancers	HUVEC	blood vessel
19	chr2:153350000-153353000	Enhancers	Psoas Muscle	Psoas
20	chr2:153350000-153354200	Weak transcription	NHDF-Ad	bronchial
21	chr2:153350200-153354000	Weak transcription	Osteobl	bone
22	chr2:153350400-153354200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:153350400-153357400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:153350800-153352000	Weak transcription	Ovary	ovary
25	chr2:153350800-153354200	Weak transcription	Left Ventricle	heart
26	chr2:153350800-153354200	Weak transcription	Right Ventricle	heart
27	chr2:153350800-153354200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:153350800-153355800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:153350800-153357000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:153350800-153360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:153351000-153352400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:153351000-153353400	Weak transcription	HepG2	liver
33	chr2:153351000-153354000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:153351000-153354000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:153351000-153355600	Weak transcription	Fetal Stomach	stomach
36	chr2:153351200-153353800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:153351200-153355400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:153351400-153352600	Weak transcription	Brain Angular Gyrus	brain
39	chr2:153351400-153354200	Weak transcription	Adipose Nuclei	Adipose
40	chr2:153351400-153355200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:153351400-153355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:153351400-153357600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:153351400-153361000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:153351600-153352000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:153351600-153352000	Weak transcription	Brain Substantia Nigra	brain
46	chr2:153351600-153352200	Weak transcription	Fetal Kidney	kidney
47	chr2:153351600-153354000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:153351600-153354200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:153351600-153354200	Weak transcription	Fetal Lung	lung
50	chr2:153351600-153354200	Weak transcription	Right Atrium	heart

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