Variant report

Variant	rs7355953
Chromosome Location	chr3:85792137-85792138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12714636	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12714640	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap]
rs13059866	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[MKK][hapmap]
rs13068138	0.84[AFR][1000 genomes]
rs13076821	1.00[YRI][hapmap]
rs13077660	1.00[CHD][hapmap];0.86[MKK][hapmap]
rs13078807	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap]
rs13085840	0.84[AFR][1000 genomes]
rs13087042	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13096280	1.00[CHD][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13098327	1.00[ASW][hapmap];0.85[MKK][hapmap]
rs13101056	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1375547	0.86[MKK][hapmap]
rs1448602	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1448608	1.00[YRI][hapmap]
rs4129299	1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4306872	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4464471	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7611991	0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs7612213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7620339	1.00[CHD][hapmap]
rs7622475	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap]
rs7628948	1.00[CHD][hapmap];0.86[MKK][hapmap]
rs7640660	1.00[CHD][hapmap]
rs9309995	1.00[CHD][hapmap]
rs9812845	0.91[TSI][hapmap]
rs9818122	1.00[CHD][hapmap]
rs9819476	1.00[CHD][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap]
rs9825885	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834708	1.00[CHD][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9852859	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs9858244	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9877300	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590905	chr3:85438564-85797093	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv1010541	chr3:85505839-85870597	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv536625	chr3:85505839-85870597	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1005102	chr3:85729640-85829412	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv532629	chr3:85763873-86608579	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv460753	chr3:85789007-85820416	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv590911	chr3:85789007-85820416	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7355953	HTR1F	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85784800-85793800	Weak transcription	Psoas Muscle	Psoas
2	chr3:85790200-85795200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:85791000-85792800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr3:85791800-85792200	Enhancers	Brain Angular Gyrus	brain
5	chr3:85792000-85792600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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