Variant report

Variant	rs642052
Chromosome Location	chr1:84683683-84683684
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11163916	1.00[EUR][1000 genomes]
rs11802352	1.00[EUR][1000 genomes]
rs11802582	1.00[EUR][1000 genomes]
rs11803089	1.00[EUR][1000 genomes]
rs3729868	1.00[EUR][1000 genomes]
rs41300502	1.00[EUR][1000 genomes]
rs41300514	1.00[EUR][1000 genomes]
rs41300516	1.00[EUR][1000 genomes]
rs41300534	1.00[EUR][1000 genomes]
rs41301174	1.00[EUR][1000 genomes]
rs624878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs633253	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs639010	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs639940	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs652426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs655181	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7524666	1.00[EUR][1000 genomes]
rs7524960	1.00[EUR][1000 genomes]
rs7532830	1.00[EUR][1000 genomes]
rs7533541	1.00[EUR][1000 genomes]
rs7538094	1.00[EUR][1000 genomes]
rs7540972	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871656	chr1:84601048-84693671	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv871643	chr1:84628655-84705481	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv871538	chr1:84633116-84717983	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv1816427	chr1:84670816-84715634	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv1823244	chr1:84670816-84715634	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	esv1824568	chr1:84670816-84715634	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	esv1822734	chr1:84678418-84715634	ZNF genes & repeats Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv1845114	chr1:84678418-84715634	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	esv1851921	chr1:84678418-84715634	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84652400-84689800	Weak transcription	Aorta	Aorta
2	chr1:84657600-84708000	Weak transcription	Left Ventricle	heart
3	chr1:84659000-84685000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:84659000-84700600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:84659000-84700800	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:84659200-84688400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:84659400-84685400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:84659800-84701400	Weak transcription	NHLF	lung
9	chr1:84660600-84686200	Weak transcription	Fetal Intestine Small	intestine
10	chr1:84660800-84688400	Weak transcription	Fetal Brain Male	brain
11	chr1:84663200-84684600	Weak transcription	Hela-S3	cervix
12	chr1:84665200-84700800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:84665400-84684000	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:84665400-84684600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:84665400-84685200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:84665400-84687600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:84665400-84700600	Weak transcription	Colonic Mucosa	Colon
18	chr1:84665400-84701000	Weak transcription	Fetal Kidney	kidney
19	chr1:84665600-84684800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:84665800-84684400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:84666000-84689800	Weak transcription	Fetal Stomach	stomach
22	chr1:84666200-84683800	Weak transcription	Fetal Lung	lung
23	chr1:84666800-84710200	Weak transcription	HSMMtube	muscle
24	chr1:84668200-84690000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:84672400-84683800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:84672400-84684200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:84672600-84685200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:84672600-84685200	Weak transcription	Fetal Intestine Large	intestine
29	chr1:84672600-84687400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:84672600-84689800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:84672600-84700600	Weak transcription	Brain Anterior Caudate	brain
32	chr1:84672600-84701000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:84672600-84711200	Weak transcription	Brain Substantia Nigra	brain
34	chr1:84672800-84684200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:84672800-84685000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:84673000-84683800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:84673000-84684000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:84673000-84685200	Weak transcription	Liver	Liver
39	chr1:84673000-84688200	Weak transcription	Brain Angular Gyrus	brain
40	chr1:84673000-84689800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:84673000-84700600	Weak transcription	HSMM	muscle
42	chr1:84673200-84684000	Weak transcription	Brain Germinal Matrix	brain
43	chr1:84673200-84684800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr1:84673200-84690000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:84675200-84712800	Weak transcription	NH-A	brain
46	chr1:84675800-84705000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:84677800-84685400	Strong transcription	Dnd41	blood
48	chr1:84679400-84685000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:84679600-84684400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:84679600-84684400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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