Variant report

Variant	rs2025607
Chromosome Location	chr1:92890344-92890345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1034219	0.93[CEU][hapmap];0.80[AMR][1000 genomes]
rs10735779	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs10747411	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782922	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10782935	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10874656	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10875348	1.00[YRI][hapmap]
rs11164605	0.85[EUR][1000 genomes]
rs11164773	0.80[AMR][1000 genomes]
rs11166568	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11166575	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226177	1.00[ASN][1000 genomes]
rs1386585	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408916	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1487537	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556562	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1570836	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1570837	0.93[CEU][hapmap]
rs17519833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17579779	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1825813	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886682	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1886683	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1906279	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031494	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2046621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2151577	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2391139	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391140	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391159	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2391160	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3103177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122320	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131815	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131816	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131824	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131831	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4247165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375281	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4568842	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs475034	1.00[ASN][1000 genomes]
rs476490	1.00[ASN][1000 genomes]
rs481384	1.00[ASN][1000 genomes]
rs4847181	0.94[CEU][hapmap]
rs4847377	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs4970696	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4970698	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4970701	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4970705	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4970706	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4970708	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4970709	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4970710	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4970712	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs524989	1.00[ASN][1000 genomes]
rs533124	1.00[ASN][1000 genomes]
rs538054	1.00[ASN][1000 genomes]
rs548141	1.00[ASN][1000 genomes]
rs566576	1.00[ASN][1000 genomes]
rs59679370	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6422512	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs6603963	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603967	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603975	0.83[EUR][1000 genomes]
rs6603979	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6603981	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6603982	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6603984	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs6603985	0.94[CEU][hapmap];0.87[AMR][1000 genomes]
rs6603987	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs6603988	0.94[CEU][hapmap]
rs6603990	0.94[CEU][hapmap]
rs6604089	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661134	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs6668685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676141	0.86[EUR][1000 genomes]
rs6676846	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6686702	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6690764	0.85[EUR][1000 genomes]
rs6692060	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692187	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6696173	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7512301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515577	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs7518357	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7520275	1.00[CHB][hapmap]
rs7536295	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7542747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545445	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547429	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7552212	0.87[EUR][1000 genomes]
rs912795	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs962221	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs962222	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs989653	0.82[CEU][hapmap];0.80[AMR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2025607	FAM69A	cis	cerebellum	SCAN
rs2025607	RPL10A	trans	cerebellum	SCAN
rs2025607	RPL5	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92885600-92891000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:92885800-92890400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr1:92889600-92890600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:92889600-92892200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:92889800-92890600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:92890000-92890400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr1:92890000-92890400	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:92890000-92890400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:92890000-92892000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:92890000-92892400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:92890200-92890400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:92890200-92890600	Enhancers	HUES64 Cell Line	embryonic stem cell

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