Variant report

Variant	rs12491888
Chromosome Location	chr3:143502226-143502227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11706563	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12488854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059339	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13066023	0.80[AMR][1000 genomes]
rs13073355	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13091085	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1868179	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166773	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166774	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361198	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs36086202	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839609	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12491888	NRG3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143492400-143513000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:143494600-143505200	Weak transcription	NHLF	lung
3	chr3:143494800-143505200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:143494800-143505200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:143494800-143505200	Weak transcription	Fetal Lung	lung
6	chr3:143494800-143505400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:143494800-143505400	Weak transcription	Right Atrium	heart
8	chr3:143494800-143515600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:143494800-143515800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:143495000-143505400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:143496200-143505200	Weak transcription	Brain Substantia Nigra	brain
12	chr3:143499000-143505200	Weak transcription	Aorta	Aorta
13	chr3:143499600-143512800	Weak transcription	Primary T cells from cord blood	blood
14	chr3:143500400-143503000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:143500600-143502800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr3:143500600-143503200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:143500800-143502400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:143500800-143503000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:143501600-143503000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:143501800-143502800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:143502000-143505400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:143502200-143503200	Enhancers	Fetal Heart	heart
23	chr3:143502200-143503400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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