Variant report

Variant	rs6696896
Chromosome Location	chr1:179501365-179501366
allele	C/T
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	STAT3	chr1:179501311-179501508	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
AXDND1	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1060775	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs10753193	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10798682	0.91[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs10798689	1.00[CHB][hapmap]
rs10913776	0.92[ASW][hapmap];0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[YRI][hapmap]
rs10913801	0.83[GIH][hapmap]
rs10913804	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913807	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11802193	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807786	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122753	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12131398	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12131400	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12136100	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs12737288	0.85[AFR][1000 genomes]
rs1328596	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1410590	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs1831180	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928001	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928004	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs2026014	1.00[JPT][hapmap]
rs3898486	0.89[GIH][hapmap]
rs4255343	1.00[JPT][hapmap]
rs4297245	0.82[GIH][hapmap]
rs4360482	0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap]
rs4421551	1.00[JPT][hapmap]
rs4606280	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs4620484	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625242	1.00[JPT][hapmap]
rs4651038	0.83[GIH][hapmap]
rs4651039	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651040	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652404	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652417	1.00[CHD][hapmap]
rs6425558	0.84[GIH][hapmap]
rs6659294	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs6659378	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662859	0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap]
rs6683623	0.84[GIH][hapmap]
rs6690605	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697280	1.00[JPT][hapmap]
rs6697373	1.00[JPT][hapmap]
rs6698201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7416021	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs749960	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7512551	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514278	0.92[ASW][hapmap];0.90[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.88[YRI][hapmap]
rs7517766	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7518557	1.00[CHB][hapmap]
rs7522064	1.00[JPT][hapmap]
rs7542099	1.00[JPT][hapmap]
rs928016	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs963062	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs964982	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787088	0.82[AFR][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	nsv522746	chr1:179501365-179518459	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6696896	TDRD5	cis	parietal	SCAN
rs6696896	RASAL2	cis	parietal	SCAN
rs6696896	FAM163A	cis	parietal	SCAN

Chromatin state (count:3 , 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	chr1:179498600-179509600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:179501200-179509600	Weak transcription	H9 Cell Line	embryonic stem cell

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