Variant report

Variant	rs2781230
Chromosome Location	chr1:10563717-10563718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10562142..10564951-chr1:10926770..10929049,2	K562	blood:
2	chr1:10549510..10553180-chr1:10560957..10564182,4	K562	blood:
3	chr1:10555587..10558317-chr1:10561654..10564400,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10864459	0.95[CEU][hapmap]
rs10864460	0.95[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs1188525	0.80[AFR][1000 genomes]
rs1188526	1.00[CEU][hapmap]
rs12028449	0.90[GIH][hapmap]
rs12038548	0.82[CHB][hapmap]
rs12065251	0.82[EUR][1000 genomes]
rs12124486	0.85[EUR][1000 genomes]
rs12375	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs12729844	0.83[EUR][1000 genomes]
rs1411402	0.90[CEU][hapmap]
rs17035305	0.90[GIH][hapmap]
rs2026792	0.82[CEU][hapmap]
rs2027087	0.83[EUR][1000 genomes]
rs2056417	0.91[CEU][hapmap];0.93[GIH][hapmap]
rs2480777	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs2483677	0.91[CEU][hapmap];0.93[GIH][hapmap]
rs2506892	0.82[CEU][hapmap]
rs2506901	1.00[CEU][hapmap]
rs2506902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2847344	0.95[CEU][hapmap]
rs34372628	0.81[EUR][1000 genomes]
rs585870	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs589400	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];0.90[YRI][hapmap]
rs596537	1.00[CEU][hapmap]
rs607941	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs616402	0.91[CEU][hapmap];0.93[GIH][hapmap]
rs616488	0.90[GIH][hapmap]
rs617728	0.83[AFR][1000 genomes]
rs620405	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs622623	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs636291	0.95[CEU][hapmap]
rs648324	1.00[CEU][hapmap]
rs648399	1.00[CEU][hapmap]
rs6540933	0.85[AFR][1000 genomes]
rs660725	1.00[CEU][hapmap]
rs662064	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs6667629	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs668805	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs669701	1.00[CEU][hapmap]
rs685746	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2781230	PEX14	cis	Lymphoblastoid	GTEx
rs2781230	PLEKHG5	cis	parietal	SCAN
rs2781230	AADACL3	cis	parietal	SCAN
rs2781230	SLC2A5	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10553000-10567200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:10554800-10568600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:10555200-10567400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:10555200-10567400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:10555200-10567400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:10555200-10568400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:10555200-10568600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:10555200-10570000	Weak transcription	Aorta	Aorta
9	chr1:10555400-10567200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:10555400-10567400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:10555600-10564200	Weak transcription	HUVEC	blood vessel
12	chr1:10555600-10567400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:10555600-10567400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:10555600-10567400	Weak transcription	A549	lung
15	chr1:10555600-10567600	Weak transcription	NH-A	brain
16	chr1:10555600-10567800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:10555600-10567800	Weak transcription	HSMM	muscle
18	chr1:10555600-10567800	Weak transcription	NHDF-Ad	bronchial
19	chr1:10555600-10568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:10555600-10568600	Weak transcription	Pancreas	Pancrea
21	chr1:10555600-10568600	Weak transcription	HSMMtube	muscle
22	chr1:10555600-10570400	Weak transcription	Brain Substantia Nigra	brain
23	chr1:10555600-10570400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:10555600-10570600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:10555800-10564400	Weak transcription	Placenta	Placenta
26	chr1:10555800-10564400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:10555800-10567200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:10555800-10567400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:10555800-10567400	Weak transcription	Osteobl	bone
30	chr1:10555800-10567800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:10555800-10567800	Weak transcription	Fetal Lung	lung
32	chr1:10555800-10568600	Weak transcription	Esophagus	oesophagus
33	chr1:10555800-10569600	Weak transcription	Colonic Mucosa	Colon
34	chr1:10555800-10570400	Weak transcription	Brain Anterior Caudate	brain
35	chr1:10556000-10567200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:10556000-10567400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:10556000-10569400	Weak transcription	Fetal Brain Female	brain
38	chr1:10556000-10570200	Weak transcription	Brain Angular Gyrus	brain
39	chr1:10556400-10564600	Weak transcription	Gastric	stomach
40	chr1:10556400-10567200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:10556400-10567400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:10556400-10567800	Weak transcription	Hela-S3	cervix
43	chr1:10556400-10570200	Weak transcription	Fetal Kidney	kidney
44	chr1:10556600-10564200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:10556600-10567200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:10556600-10567200	Weak transcription	K562	blood
47	chr1:10556600-10568000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:10556600-10568600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:10556600-10570000	Weak transcription	Right Ventricle	heart
50	chr1:10556600-10570400	Weak transcription	Brain Cingulate Gyrus	brain

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