Variant report

Variant	rs12130380
Chromosome Location	chr1:85901309-85901310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10158674	0.81[CEU][hapmap]
rs11161599	0.81[CEU][hapmap]
rs11161614	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161615	0.81[CEU][hapmap]
rs11161616	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161617	0.90[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12049529	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12118950	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs12123745	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12125900	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12128907	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12129013	0.91[CEU][hapmap];0.85[AMR][1000 genomes]
rs12129502	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12130145	0.82[CEU][hapmap]
rs12131926	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12132677	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs12133722	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12135333	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12138852	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12139958	0.86[EUR][1000 genomes]
rs12140170	0.86[EUR][1000 genomes]
rs12140457	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs12140935	0.86[EUR][1000 genomes]
rs12717763	0.81[CEU][hapmap]
rs12736004	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12743049	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12758237	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12758768	0.84[EUR][1000 genomes]
rs1498374	0.81[CEU][hapmap]
rs1608536	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs17384381	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17388521	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2076699	0.81[CEU][hapmap]
rs2300639	0.82[CEU][hapmap]
rs35193119	0.86[EUR][1000 genomes]
rs36110608	0.85[EUR][1000 genomes]
rs986639	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85874000-85903800	Weak transcription	NHLF	lung
2	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:85874400-85903600	Weak transcription	HepG2	liver
4	chr1:85874400-85904200	Weak transcription	NH-A	brain
5	chr1:85886400-85903800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:85886400-85914200	Weak transcription	HSMMtube	muscle
7	chr1:85886800-85903800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:85887600-85902200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:85887600-85903400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:85890400-85902200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:85892200-85906200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:85893800-85906200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:85893800-85916800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:85894400-85903600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:85894600-85903600	Weak transcription	Adipose Nuclei	Adipose
16	chr1:85894600-85903800	Weak transcription	HUVEC	blood vessel
17	chr1:85894600-85904200	Weak transcription	Fetal Intestine Small	intestine
18	chr1:85897000-85904200	Weak transcription	Fetal Intestine Large	intestine
19	chr1:85897800-85904200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:85897800-85904800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:85898000-85902200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:85898200-85903600	Weak transcription	Liver	Liver
23	chr1:85899200-85902000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:85899200-85902200	Weak transcription	Osteobl	bone
25	chr1:85899200-85903600	Weak transcription	NHDF-Ad	bronchial
26	chr1:85899200-85914800	Weak transcription	Esophagus	oesophagus
27	chr1:85899400-85902200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:85899400-85903600	Weak transcription	HSMM	muscle
29	chr1:85901200-85901400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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