Variant report

Variant	rs2209922
Chromosome Location	chr1:179499839-179499840
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:179499408-179499895	H1-hESC	embryonic stem cell:	n/a	chr1:179499666-179499677
2	MAX	chr1:179499506-179499902	H1-hESC	embryonic stem cell:	n/a	chr1:179499666-179499677
3	E2F6	chr1:179499386-179499935	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr1:179499525-179499871	H1-hESC	embryonic stem cell:	n/a	chr1:179499666-179499677
5	E2F6	chr1:179499496-179499904	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179497716..179500017-chr1:179555604..179558025,2	MCF-7	breast:

Variant related genes	Relation type
AXDND1	TF binding region
ENSG00000227141	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10157829	0.81[JPT][hapmap]
rs10494517	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494518	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798709	0.81[JPT][hapmap]
rs10913765	0.82[CHB][hapmap]
rs10913815	0.82[CHD][hapmap]
rs10913863	0.81[JPT][hapmap]
rs11577538	0.87[ASW][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.95[MKK][hapmap];0.88[ASN][1000 genomes]
rs11578278	0.81[JPT][hapmap]
rs11581440	0.85[ASN][1000 genomes]
rs11581470	0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs11585517	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs11586725	0.91[JPT][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs11808258	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12021675	0.80[JPT][hapmap]
rs12035247	0.81[JPT][hapmap]
rs12042409	0.81[JPT][hapmap]
rs12566954	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743373	0.82[CHB][hapmap]
rs12749731	0.81[CHB][hapmap]
rs12757065	0.82[CHB][hapmap]
rs1410585	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1410587	0.85[CHD][hapmap]
rs1410588	0.82[CHD][hapmap]
rs1410593	0.86[JPT][hapmap]
rs16854042	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs16854244	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854337	0.86[ASN][1000 genomes]
rs2149399	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2274622	0.87[ASW][hapmap];0.91[JPT][hapmap];0.87[MKK][hapmap];0.87[YRI][hapmap]
rs2274626	0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2296960	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3754132	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3765547	0.91[JPT][hapmap];0.85[YRI][hapmap]
rs4072098	0.81[JPT][hapmap]
rs4072451	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4072452	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4111171	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41267596	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4400577	0.82[CHB][hapmap]
rs4408116	0.81[JPT][hapmap]
rs4424468	0.82[CHB][hapmap]
rs4474210	0.81[JPT][hapmap]
rs4651025	0.82[CHB][hapmap]
rs4651041	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4651042	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651045	0.81[JPT][hapmap]
rs4652369	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4652374	0.82[CHB][hapmap]
rs4652380	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4652400	0.87[ASN][1000 genomes]
rs4652405	0.85[ASN][1000 genomes]
rs4652406	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652407	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652408	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652411	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4652412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4652432	0.81[JPT][hapmap]
rs4652433	0.81[JPT][hapmap]
rs4652434	0.81[JPT][hapmap]
rs4652438	0.81[JPT][hapmap]
rs55908143	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071531	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56237305	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57340322	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425557	0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap]
rs6425571	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425572	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425574	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425580	0.81[JPT][hapmap]
rs6425581	0.81[JPT][hapmap]
rs6425585	0.81[JPT][hapmap]
rs6425588	0.81[JPT][hapmap]
rs6657452	0.90[ASN][1000 genomes]
rs6658180	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664339	0.86[CHB][hapmap]
rs6666455	0.81[JPT][hapmap]
rs6668120	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6674086	1.00[ASW][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs6678667	0.82[CHB][hapmap]
rs6679542	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs6689426	0.86[JPT][hapmap]
rs6690348	0.82[CHB][hapmap]
rs6691856	0.81[JPT][hapmap]
rs6692069	0.81[JPT][hapmap]
rs6693627	0.82[CHB][hapmap]
rs6700149	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs72704467	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72704477	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7413415	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7512638	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs7519436	0.81[JPT][hapmap]
rs7519700	0.88[ASN][1000 genomes]
rs7529107	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7541890	0.91[JPT][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs7541899	0.88[ASN][1000 genomes]
rs7543334	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7547484	0.81[JPT][hapmap]
rs7548654	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551440	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7551610	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs913514	0.83[JPT][hapmap]
rs9286930	0.86[ASN][1000 genomes]
rs962428	0.90[ASN][1000 genomes]
rs964983	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964984	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2209922	TDRD5	cis	parietal	SCAN
rs2209922	TDRD5	cis	Artery Tibial	GTEx
rs2209922	TDRD5	cis	Nerve Tibial	GTEx
rs2209922	TDRD5	cis	Adipose Subcutaneous	GTEx
rs2209922	TDRD5	cis	Esophagus Mucosa	GTEx
rs2209922	TDRD5	cis	Artery Aorta	GTEx
rs2209922	GPR52	cis	cerebellum	SCAN
rs2209922	TDRD5	cis	Thyroid	GTEx
rs2209922	SOAT1	cis	cerebellum	SCAN
rs2209922	RASAL2	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179487200-179515000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:179498600-179500000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr1:179498600-179509600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:179499000-179500200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr1:179499600-179500000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:179499600-179500000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:179499600-179500200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:179499600-179500200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:179499600-179500600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr1:179499800-179500000	Enhancers	HUES48 Cell Line	embryonic stem cell

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