Variant report

Variant	rs662064
Chromosome Location	chr1:10557251-10557252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10494447..10496934-chr1:10557119..10558768,2	MCF-7	breast:
2	chr1:10555587..10558317-chr1:10561654..10564400,3	K562	blood:

Variant related genes	Relation type
ENSG00000251503	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10864458	0.86[EUR][1000 genomes]
rs10864459	0.95[CEU][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs10864460	0.95[CEU][hapmap]
rs11121587	0.82[CHB][hapmap]
rs1152739	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1188525	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1188526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1188528	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1188529	0.88[EUR][1000 genomes]
rs12028449	0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs12375	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs1307489	0.92[CHB][hapmap]
rs1307490	0.84[CHB][hapmap]
rs1307494	0.84[CHB][hapmap]
rs1307497	0.84[CHB][hapmap]
rs1308520	0.92[CHB][hapmap]
rs1411402	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1632108	0.97[EUR][1000 genomes]
rs17035305	0.82[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs2026792	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2056417	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2480777	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs2480782	0.82[CHB][hapmap]
rs2480784	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2480785	0.86[EUR][1000 genomes]
rs2483677	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2483686	0.92[CHB][hapmap]
rs2506880	0.84[EUR][1000 genomes]
rs2506892	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2506901	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2506902	1.00[CEU][hapmap]
rs2781230	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs2781232	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2847337	0.92[CHB][hapmap]
rs2847344	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs544289	0.84[CHB][hapmap]
rs585870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587916	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs589400	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs596537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597438	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs616402	0.91[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs616488	0.91[GIH][hapmap];0.82[TSI][hapmap]
rs617728	0.87[EUR][1000 genomes]
rs620405	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636291	0.95[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs648324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648399	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];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs652771	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6540931	0.90[CHB][hapmap]
rs6540933	0.98[EUR][1000 genomes]
rs657244	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs660725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687430	0.84[CHD][hapmap]
rs668805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs669701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs683864	0.97[EUR][1000 genomes]
rs685746	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs944973	0.84[CHB][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs662064	AADACL3	cis	parietal	SCAN
rs662064	SLC2A5	cis	parietal	SCAN
rs662064	PLEKHG5	cis	parietal	SCAN

Chromatin state (count:114 , 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	chr1:10555400-10557600	Strong transcription	HepG2	liver
10	chr1:10555400-10567200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:10555400-10567400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:10555600-10557400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:10555600-10557600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:10555600-10557600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:10555600-10557600	Strong transcription	Fetal Stomach	stomach
16	chr1:10555600-10557800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:10555600-10557800	Strong transcription	Brain Germinal Matrix	brain
18	chr1:10555600-10558600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:10555600-10559000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:10555600-10560800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:10555600-10561000	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:10555600-10564200	Weak transcription	HUVEC	blood vessel
23	chr1:10555600-10567400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:10555600-10567400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:10555600-10567400	Weak transcription	A549	lung
26	chr1:10555600-10567600	Weak transcription	NH-A	brain
27	chr1:10555600-10567800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:10555600-10567800	Weak transcription	HSMM	muscle
29	chr1:10555600-10567800	Weak transcription	NHDF-Ad	bronchial
30	chr1:10555600-10568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:10555600-10568600	Weak transcription	Pancreas	Pancrea
32	chr1:10555600-10568600	Weak transcription	HSMMtube	muscle
33	chr1:10555600-10570400	Weak transcription	Brain Substantia Nigra	brain
34	chr1:10555600-10570400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:10555600-10570600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:10555800-10557400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:10555800-10557600	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:10555800-10559200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:10555800-10559200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:10555800-10564400	Weak transcription	Placenta	Placenta
41	chr1:10555800-10564400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:10555800-10567200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:10555800-10567400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:10555800-10567400	Weak transcription	Osteobl	bone
45	chr1:10555800-10567800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:10555800-10567800	Weak transcription	Fetal Lung	lung
47	chr1:10555800-10568600	Weak transcription	Esophagus	oesophagus
48	chr1:10555800-10569600	Weak transcription	Colonic Mucosa	Colon
49	chr1:10555800-10570400	Weak transcription	Brain Anterior Caudate	brain
50	chr1:10556000-10557400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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