Variant report

Variant	rs1404431
Chromosome Location	chr7:103436603-103436604
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	chr7:103432622..103435119-chr7:103435202..103437569,2	K562	blood:
2	chr7:103423396..103425978-chr7:103435870..103438560,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10487171	0.84[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs10953393	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11973815	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11974819	0.84[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12531131	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs141473	0.83[CHD][hapmap]
rs17155576	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs17156394	0.83[JPT][hapmap];0.81[YRI][hapmap]
rs1963647	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2214943	0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs2237636	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs262375	0.85[MEX][hapmap]
rs3819484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3819489	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3847070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140848	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs4729931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729932	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56106813	0.82[ASN][1000 genomes]
rs58420913	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58581358	0.84[ASN][1000 genomes]
rs60403171	0.96[ASN][1000 genomes]
rs60851159	0.81[ASN][1000 genomes]
rs61124913	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67342215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67399010	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67649823	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73180133	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73180201	0.81[ASN][1000 genomes]
rs73181905	0.81[ASN][1000 genomes]
rs73412894	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745540	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878458	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427799	chr7:103250733-103454202	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1016328	chr7:103396911-103443565	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv539048	chr7:103396911-103443565	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv1843940	chr7:103421702-103590285	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1404431	TSC22D4	cis	cerebellum	SCAN
rs1404431	ATXN7L1	cis	cerebellum	SCAN
rs1404431	CDHR3	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103433600-103437000	Enhancers	HepG2	liver
2	chr7:103434800-103436800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:103434800-103438800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:103435800-103440000	Weak transcription	K562	blood
5	chr7:103436000-103436800	Enhancers	Brain Germinal Matrix	brain

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