Variant report

Variant	rs9844512
Chromosome Location	chr3:85544070-85544071
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10154865	0.87[AMR][1000 genomes]
rs10433498	0.81[EUR][1000 genomes]
rs11127891	0.86[EUR][1000 genomes]
rs11712915	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713902	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11716233	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12498010	0.91[CEU][hapmap]
rs12633762	0.86[EUR][1000 genomes]
rs12714629	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13068434	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13070166	0.92[EUR][1000 genomes]
rs13076830	0.87[AMR][1000 genomes]
rs13077660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][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];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084531	0.93[EUR][1000 genomes]
rs13092437	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096280	1.00[CHD][hapmap];0.87[MKK][hapmap]
rs13353478	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1368739	0.86[EUR][1000 genomes]
rs1368740	0.87[EUR][1000 genomes]
rs1368743	0.81[EUR][1000 genomes]
rs1375547	0.89[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1375553	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449404	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821349	0.86[TSI][hapmap]
rs2117151	0.81[CEU][hapmap]
rs2196096	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2196097	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2196098	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2326313	0.81[EUR][1000 genomes]
rs35344466	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887138	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772991	0.84[EUR][1000 genomes]
rs6808159	0.82[EUR][1000 genomes]
rs6809805	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71626887	0.82[EUR][1000 genomes]
rs7628948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][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];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650834	0.82[EUR][1000 genomes]
rs9309977	0.81[EUR][1000 genomes]
rs9309981	0.91[TSI][hapmap]
rs9309982	0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs9810724	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs9814516	0.91[CEU][hapmap]
rs9819476	1.00[ASW][hapmap];1.00[CHD][hapmap];0.87[MKK][hapmap]
rs9819830	0.86[TSI][hapmap]
rs9820228	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9822731	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs9826458	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833314	0.82[EUR][1000 genomes]
rs9834708	1.00[CHD][hapmap];0.91[MKK][hapmap]
rs9838811	0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs9841144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9851444	0.88[CEU][hapmap]
rs9854869	0.87[AMR][1000 genomes]
rs9863620	0.81[EUR][1000 genomes]
rs9865745	0.82[EUR][1000 genomes]
rs9866322	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866761	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870448	0.87[AMR][1000 genomes]
rs9873400	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879025	0.81[EUR][1000 genomes]
rs9880397	1.00[CHD][hapmap];1.00[YRI][hapmap]
rs9880919	0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1002238	chr3:85357855-85719373	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
4	nsv536619	chr3:85357855-85719373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590904	chr3:85438564-85551403	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	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
7	nsv998829	chr3:85449960-85641099	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv536622	chr3:85449960-85641099	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv526621	chr3:85470642-85667683	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1013601	chr3:85489536-85570465	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv536624	chr3:85489536-85570465	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
12	nsv1009927	chr3:85497666-85669155	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
13	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
14	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
15	esv2762338	chr3:85520915-85577233	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
16	nsv1009804	chr3:85521984-85581386	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
17	nsv536626	chr3:85527837-85578368	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
18	nsv1002139	chr3:85534559-85630146	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1006433	chr3:85535783-85631667	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv590906	chr3:85539816-85626054	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9844512	HTR1F	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85542800-85544400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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