Variant report

Variant	rs10514642
Chromosome Location	chr2:210340967-210340968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10514643	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10514644	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11892351	0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11896384	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12986617	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12990915	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12991864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12992067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12992468	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12993084	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12993506	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12993627	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12995238	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12995429	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13000895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13000954	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13002255	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13014332	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13015584	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13016157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13022394	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13022724	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13023473	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13025539	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13027122	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13027599	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13027724	1.00[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13027957	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13030241	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13036178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842929	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842934	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843177	0.81[TSI][hapmap]
rs17236751	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17237719	1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17237893	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17238539	1.00[CEU][hapmap]
rs17238784	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs17308504	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs17316862	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17316904	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17316974	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17317100	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17317170	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs288063	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34128824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34156640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34923027	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34968429	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35273017	0.85[EUR][1000 genomes]
rs35388880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35553764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35781477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35997966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36003754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36101555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6756379	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71420756	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71420757	1.00[AMR][1000 genomes];1.00[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10514642	PRAC	trans	lymphoblastoid	seeQTL
rs10514642	CCDC85A	trans	lymphoblastoid	seeQTL
rs10514642	HGF	trans	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210319800-210341000	Weak transcription	Fetal Brain Female	brain
2	chr2:210332800-210351200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:210335600-210342400	Enhancers	Hela-S3	cervix
4	chr2:210337800-210341200	Weak transcription	Brain Anterior Caudate	brain
5	chr2:210338000-210341200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:210338000-210341200	Weak transcription	HSMMtube	muscle
7	chr2:210338000-210357400	Weak transcription	Aorta	Aorta
8	chr2:210339200-210359800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:210339200-210360000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:210339400-210341000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:210339400-210341000	Weak transcription	Osteobl	bone
12	chr2:210339400-210341200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:210339400-210341600	Weak transcription	NH-A	brain
14	chr2:210339400-210342000	Enhancers	Fetal Brain Male	brain
15	chr2:210339600-210341000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:210339600-210341200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:210339600-210341200	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:210339600-210341400	Weak transcription	NHLF	lung
19	chr2:210339800-210344600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:210340000-210341800	Enhancers	Brain Germinal Matrix	brain
21	chr2:210340400-210342000	Enhancers	HUVEC	blood vessel
22	chr2:210340600-210341600	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr2:210340800-210341200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:210340800-210341600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr2:210340800-210341800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:210340800-210341800	Enhancers	Muscle Satellite Cultured Cells	--

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