Variant report

Variant	rs10514643
Chromosome Location	chr2:210378048-210378049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:210352493..210354448-chr2:210377113..210379529,2	K562	blood:
2	chr2:210372196..210374156-chr2:210376464..210379426,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10514642	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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12986617	1.00[CEU][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12990915	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12991864	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12992067	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12992468	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12993084	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12993506	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12993627	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12995238	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12995429	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13000895	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13000954	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13002255	1.00[CEU][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13014332	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13015584	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13016157	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13022394	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13022724	1.00[CEU][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13023473	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13025539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13027122	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13027599	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13027724	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]
rs13027957	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13030241	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13036178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842909	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842929	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842934	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];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];0.89[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17237893	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17238539	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs17238784	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs17308504	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs17316862	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17316904	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17316974	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17317100	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17317170	1.00[CEU][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34923027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34968429	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35273017	0.85[EUR][1000 genomes]
rs35388880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35553764	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35781477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35997966	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36003754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36101555	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6756379	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71420756	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71420757	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	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
rs10514643	HGF	trans	lymphoblastoid	seeQTL
rs10514643	PRAC	trans	lymphoblastoid	seeQTL
rs10514643	CCDC85A	trans	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210363600-210378400	Weak transcription	Brain Germinal Matrix	brain
2	chr2:210364600-210387600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:210364600-210392200	Weak transcription	Pancreas	Pancrea
4	chr2:210366600-210387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:210371400-210391000	Weak transcription	Aorta	Aorta
6	chr2:210372800-210381000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:210373000-210380000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:210377400-210378200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:210377400-210378200	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:210377400-210378800	Enhancers	Fetal Brain Male	brain
11	chr2:210377400-210378800	Enhancers	Fetal Brain Female	brain
12	chr2:210377600-210378200	Enhancers	Primary B cells from cord blood	blood
13	chr2:210377600-210378200	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr2:210377600-210378800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:210378000-210378200	Enhancers	Right Atrium	heart
16	chr2:210378000-210380200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:210378000-210384000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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