Variant report

Variant	rs12490327
Chromosome Location	chr3:54739178-54739179
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	chr3:54738031..54740045-chr3:54741949..54744426,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10510773	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs12488046	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12490953	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12496821	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs13060843	0.81[ASN][1000 genomes]
rs13068008	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap]
rs13070126	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081682	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13083683	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13084347	0.88[CHD][hapmap]
rs13084602	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086256	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13088416	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13095178	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13096365	0.87[ASN][1000 genomes]
rs13100029	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs1344671	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs1520575	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17815840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1829549	0.85[ASN][1000 genomes]
rs1882320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1882322	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs1921548	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2099019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs36061401	0.88[ASN][1000 genomes]
rs3852006	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3864001	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3868872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3906509	0.89[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4083342	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6798481	0.85[ASN][1000 genomes]
rs6808464	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72870697	0.81[ASN][1000 genomes]
rs7618235	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7623961	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636321	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12490327	RFT1	cis	cerebellum	SCAN
rs12490327	PPM1M	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54713600-54743400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54737000-54740600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:54737200-54740200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:54737400-54739600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr3:54737400-54739800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:54737600-54739400	Enhancers	Brain Anterior Caudate	brain
7	chr3:54737600-54739600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:54737600-54739600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:54737600-54742200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:54737800-54739800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:54737800-54741800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:54738000-54739800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:54738000-54740000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:54738000-54742400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:54738000-54743400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:54738200-54739200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:54738200-54743600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:54738400-54739200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:54738400-54741600	Enhancers	Fetal Muscle Leg	muscle
20	chr3:54738600-54741800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:54738800-54739600	Enhancers	Ovary	ovary
22	chr3:54738800-54739800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:54739000-54741600	Weak transcription	H9 Cell Line	embryonic stem cell

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