Variant report

Variant	rs7528642
Chromosome Location	chr1:209916598-209916599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr1:209916257-209916985	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr1:209916401-209917066	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:209916209-209916951	U87	brain:	n/a	n/a
4	NFIC	chr1:209916299-209917074	SK-N-SH	brain:	n/a	n/a
5	MYC	chr1:209916582-209916711	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:209916235-209916931	U87	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000236136	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10082248	1.00[CEU][hapmap]
rs11119345	0.85[EUR][1000 genomes]
rs12058100	0.85[EUR][1000 genomes]
rs12561766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015076	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038053	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076149	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2076151	0.82[AMR][1000 genomes]
rs2142860	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2235370	1.00[EUR][1000 genomes]
rs2236902	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2272866	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2282740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294406	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4329516	1.00[CEU][hapmap]
rs4545339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4844488	0.86[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs4844491	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4844893	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4844894	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56822893	0.85[EUR][1000 genomes]
rs57283682	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58788672	0.83[EUR][1000 genomes]
rs6540547	1.00[CEU][hapmap]
rs6694238	1.00[CEU][hapmap]
rs7515014	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517461	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532021	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532709	0.87[YRI][hapmap];0.94[AFR][1000 genomes]
rs846908	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209907600-209920800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209914000-209917200	Enhancers	Liver	Liver
3	chr1:209914200-209916800	Enhancers	Fetal Intestine Large	intestine
4	chr1:209914200-209916800	Enhancers	Left Ventricle	heart
5	chr1:209914600-209916600	Enhancers	Fetal Intestine Small	intestine
6	chr1:209914600-209917000	Enhancers	Ovary	ovary
7	chr1:209914800-209917800	Enhancers	Pancreas	Pancrea
8	chr1:209914800-209917800	Enhancers	Right Atrium	heart
9	chr1:209915200-209916800	Enhancers	Fetal Stomach	stomach
10	chr1:209915200-209916800	Enhancers	Gastric	stomach
11	chr1:209915200-209917200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:209915200-209920800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:209915200-209921000	Weak transcription	Spleen	Spleen
14	chr1:209915400-209916600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:209915400-209917200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:209915400-209917600	Weak transcription	Lung	lung
17	chr1:209915400-209918600	Enhancers	Brain Angular Gyrus	brain
18	chr1:209915400-209920400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:209915400-209920800	Weak transcription	Esophagus	oesophagus
20	chr1:209915600-209920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:209915800-209916600	Enhancers	NHDF-Ad	bronchial
22	chr1:209915800-209916800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:209915800-209917000	Enhancers	HMEC	breast
24	chr1:209915800-209917200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr1:209915800-209917200	Enhancers	Right Ventricle	heart
26	chr1:209915800-209917200	Enhancers	NH-A	brain
27	chr1:209915800-209919800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:209916000-209917000	Enhancers	Brain Anterior Caudate	brain
29	chr1:209916000-209920800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:209916000-209920800	Weak transcription	GM12878-XiMat	blood
31	chr1:209916200-209916800	Enhancers	Duodenum Mucosa	Duodenum
32	chr1:209916200-209916800	Enhancers	Fetal Lung	lung
33	chr1:209916200-209917200	Enhancers	NHLF	lung
34	chr1:209916200-209917400	Enhancers	Brain Hippocampus Middle	brain
35	chr1:209916200-209917800	Enhancers	Fetal Heart	heart
36	chr1:209916200-209919800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:209916200-209920200	Weak transcription	Adipose Nuclei	Adipose
38	chr1:209916400-209916600	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr1:209916400-209916600	Enhancers	Fetal Muscle Trunk	muscle
40	chr1:209916400-209916600	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr1:209916400-209916800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:209916400-209916800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:209916400-209916800	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:209916400-209917200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:209916400-209917200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:209916400-209917200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:209916400-209917200	Enhancers	Osteobl	bone
48	chr1:209916400-209917400	Enhancers	Brain Cingulate Gyrus	brain
49	chr1:209916400-209918400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:209916400-209918800	Enhancers	Brain Inferior Temporal Lobe	brain

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