Variant report

Variant	rs997109
Chromosome Location	chr2:210341429-210341430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10173260	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10208979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1031461	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10737939	0.97[ASN][1000 genomes]
rs10737940	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11686346	0.95[ASN][1000 genomes]
rs11687844	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12052799	0.98[ASN][1000 genomes]
rs12053460	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2123700	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2198475	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2198476	0.95[ASN][1000 genomes]
rs2198477	0.95[ASN][1000 genomes]
rs2198478	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2219085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2365657	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2365658	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs288046	0.89[ASN][1000 genomes]
rs288048	0.88[EUR][1000 genomes]
rs288049	0.88[EUR][1000 genomes]
rs288052	0.96[CEU][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs288062	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs288064	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs288065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs288067	0.94[ASN][1000 genomes]
rs288068	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2886435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2886436	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4673481	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4673482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6435530	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6435531	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6728378	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6738205	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6740822	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7559831	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7561678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7562585	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7568354	0.98[ASN][1000 genomes]
rs7574854	0.92[ASN][1000 genomes]
rs7580512	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7586196	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7593377	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7601095	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs852734	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9288409	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	nsv834518	chr2:210204958-210372744	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv834519	chr2:210271017-210400153	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs997109	UNC80	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210332800-210351200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:210335600-210342400	Enhancers	Hela-S3	cervix
3	chr2:210338000-210357400	Weak transcription	Aorta	Aorta
4	chr2:210339200-210359800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:210339200-210360000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:210339400-210341600	Weak transcription	NH-A	brain
7	chr2:210339400-210342000	Enhancers	Fetal Brain Male	brain
8	chr2:210339800-210344600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:210340000-210341800	Enhancers	Brain Germinal Matrix	brain
10	chr2:210340400-210342000	Enhancers	HUVEC	blood vessel
11	chr2:210340600-210341600	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr2:210340800-210341600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr2:210340800-210341800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:210340800-210341800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:210341000-210341600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:210341000-210341600	Enhancers	Fetal Heart	heart
17	chr2:210341000-210341800	Enhancers	Osteobl	bone
18	chr2:210341200-210341800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:210341200-210341800	Enhancers	HSMMtube	muscle
20	chr2:210341200-210342000	Enhancers	Brain Anterior Caudate	brain
21	chr2:210341200-210342000	Enhancers	Colon Smooth Muscle	Colon
22	chr2:210341200-210342000	Enhancers	Fetal Muscle Leg	muscle
23	chr2:210341200-210342400	Enhancers	Fetal Kidney	kidney
24	chr2:210341400-210341600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:210341400-210342000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:210341400-210342000	Enhancers	NHLF	lung
27	chr2:210341400-210342200	Enhancers	Fetal Brain Female	brain

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