Variant report

Variant	rs12135679
Chromosome Location	chr1:84436357-84436358
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10489508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163863	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163864	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116522	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116857	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119424	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12119854	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120380	1.00[ASN][1000 genomes]
rs12120801	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120905	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123323	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125111	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125251	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125649	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12126397	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126515	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127526	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127657	1.00[ASN][1000 genomes]
rs12128942	1.00[ASN][1000 genomes]
rs12129276	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133949	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139383	1.00[ASN][1000 genomes]
rs12140562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140964	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141004	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141166	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142059	1.00[ASN][1000 genomes]
rs12142220	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12142873	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12142944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12143951	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12144066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144704	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145472	1.00[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408475	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17130437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17130475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17475494	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534879	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925712	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293003	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293005	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423448	1.00[ASN][1000 genomes]
rs41525348	1.00[ASN][1000 genomes]
rs4258240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4387198	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45515591	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159052	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700983	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9645391	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9645396	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9645397	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871551	chr1:84354464-84453223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84416800-84436400	Weak transcription	Psoas Muscle	Psoas
2	chr1:84425200-84453200	Weak transcription	NHLF	lung
3	chr1:84426200-84452200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:84427800-84436400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:84427800-84444600	Weak transcription	HSMM	muscle
6	chr1:84429000-84436400	Weak transcription	Pancreas	Pancrea
7	chr1:84429200-84445400	Weak transcription	Aorta	Aorta
8	chr1:84430200-84441600	Weak transcription	HSMMtube	muscle
9	chr1:84430400-84447400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:84431600-84437400	Enhancers	Brain Substantia Nigra	brain
11	chr1:84433600-84436400	Weak transcription	Right Atrium	heart
12	chr1:84433800-84446000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:84435600-84437000	Enhancers	Fetal Brain Female	brain
14	chr1:84435800-84436400	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr1:84435800-84436600	Enhancers	Brain Angular Gyrus	brain
16	chr1:84435800-84436800	Enhancers	Brain Cingulate Gyrus	brain
17	chr1:84435800-84436800	Enhancers	Fetal Heart	heart
18	chr1:84436000-84436400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:84436000-84437000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:84436000-84437400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr1:84436200-84436400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:84436200-84437000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:84436200-84437000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:84436200-84437000	Genic enhancers	Brain Anterior Caudate	brain
25	chr1:84436200-84437200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:84436200-84437200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr1:84436200-84437200	Enhancers	Brain Hippocampus Middle	brain

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