Variant report

Variant	rs12564698
Chromosome Location	chr1:85862711-85862712
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11582061	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11588128	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12564550	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568573	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17127199	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2284800	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2935	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3813600	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56215900	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56216312	0.87[EUR][1000 genomes]
rs67644506	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72722665	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72722677	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72724632	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7520993	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3393958	chr1:85857980-85874598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85839800-85864200	Weak transcription	Aorta	Aorta
2	chr1:85845000-85870000	Weak transcription	HSMMtube	muscle
3	chr1:85849400-85863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:85850800-85863600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:85852400-85863400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:85852400-85864200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:85853800-85864200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:85854600-85862800	Weak transcription	Liver	Liver
9	chr1:85854600-85863400	Weak transcription	HUVEC	blood vessel
10	chr1:85855200-85870000	Weak transcription	Fetal Stomach	stomach
11	chr1:85856000-85872800	Weak transcription	Fetal Intestine Small	intestine
12	chr1:85858800-85863600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:85859400-85865000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:85860200-85862800	Weak transcription	NHLF	lung
15	chr1:85860600-85862800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:85861000-85863600	Weak transcription	HSMM	muscle
17	chr1:85861200-85862800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:85861600-85865800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:85861800-85863000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:85861800-85865800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:85862000-85863000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:85862000-85863400	Weak transcription	NH-A	brain
23	chr1:85862000-85863800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:85862000-85864800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:85862200-85863400	Weak transcription	Psoas Muscle	Psoas
26	chr1:85862200-85863400	Weak transcription	NHDF-Ad	bronchial
27	chr1:85862200-85863600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:85862200-85874600	Weak transcription	Pancreas	Pancrea
29	chr1:85862400-85863200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:85862400-85863400	Weak transcription	Osteobl	bone
31	chr1:85862600-85863200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:85862600-85863200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:85862600-85863400	Weak transcription	Ovary	ovary
34	chr1:85862600-85863800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:85862600-85864400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:85862600-85865000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:85862600-85869000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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