Variant report

Variant	rs616402
Chromosome Location	chr1:10566272-10566273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10532781..10535521-chr1:10564709..10566655,2	MCF-7	breast:
2	chr1:10566008..10570273-chr1:10573569..10578315,6	K562	blood:

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10864459	0.86[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs10864460	0.86[CEU][hapmap]
rs11121587	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs1152739	0.85[EUR][1000 genomes]
rs1188525	0.88[EUR][1000 genomes]
rs1188526	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs12028449	0.86[CEU][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs12375	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs12741973	0.88[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs1411402	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1632108	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17035305	0.82[CEU][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2026792	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs2056417	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2150038	0.89[EUR][1000 genomes]
rs2480777	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2480785	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483677	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2506880	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2506889	0.90[EUR][1000 genomes]
rs2506892	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs2506896	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2506901	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2506902	0.90[CEU][hapmap]
rs2781230	0.91[CEU][hapmap];0.93[GIH][hapmap]
rs2781232	0.88[EUR][1000 genomes]
rs2847344	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34575776	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846235	0.87[EUR][1000 genomes]
rs585870	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs587916	0.88[EUR][1000 genomes]
rs589400	0.91[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs596537	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs597438	0.88[EUR][1000 genomes]
rs607941	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs616488	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs617728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs620405	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs622623	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs636291	0.86[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs647281	0.89[CHB][hapmap]
rs648324	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs648399	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs652771	0.88[EUR][1000 genomes]
rs6540933	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs660725	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs662064	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs668805	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs669701	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs67488812	0.88[EUR][1000 genomes]
rs683864	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs685746	0.86[CEU][hapmap]
rs9430149	0.88[EUR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs616402	AADACL3	cis	parietal	SCAN
rs616402	PEX14	cis	multi-tissue	Pritchard
rs616402	SLC2A5	cis	parietal	SCAN

Chromatin state (count:113 , 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	chr1:10555600-10567400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:10555600-10567400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:10555600-10567400	Weak transcription	A549	lung
14	chr1:10555600-10567600	Weak transcription	NH-A	brain
15	chr1:10555600-10567800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:10555600-10567800	Weak transcription	HSMM	muscle
17	chr1:10555600-10567800	Weak transcription	NHDF-Ad	bronchial
18	chr1:10555600-10568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:10555600-10568600	Weak transcription	Pancreas	Pancrea
20	chr1:10555600-10568600	Weak transcription	HSMMtube	muscle
21	chr1:10555600-10570400	Weak transcription	Brain Substantia Nigra	brain
22	chr1:10555600-10570400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:10555600-10570600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:10555800-10567200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:10555800-10567400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:10555800-10567400	Weak transcription	Osteobl	bone
27	chr1:10555800-10567800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:10555800-10567800	Weak transcription	Fetal Lung	lung
29	chr1:10555800-10568600	Weak transcription	Esophagus	oesophagus
30	chr1:10555800-10569600	Weak transcription	Colonic Mucosa	Colon
31	chr1:10555800-10570400	Weak transcription	Brain Anterior Caudate	brain
32	chr1:10556000-10567200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:10556000-10567400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:10556000-10569400	Weak transcription	Fetal Brain Female	brain
35	chr1:10556000-10570200	Weak transcription	Brain Angular Gyrus	brain
36	chr1:10556400-10567200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:10556400-10567400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:10556400-10567800	Weak transcription	Hela-S3	cervix
39	chr1:10556400-10570200	Weak transcription	Fetal Kidney	kidney
40	chr1:10556600-10567200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:10556600-10567200	Weak transcription	K562	blood
42	chr1:10556600-10568000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:10556600-10568600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:10556600-10570000	Weak transcription	Right Ventricle	heart
45	chr1:10556600-10570400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:10556600-10570400	Weak transcription	Stomach Mucosa	stomach
47	chr1:10556800-10567400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:10556800-10567600	Weak transcription	Primary T cells from cord blood	blood
49	chr1:10556800-10567800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:10556800-10567800	Weak transcription	Colon Smooth Muscle	Colon

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