Variant report

Variant	rs6768632
Chromosome Location	chr3:68185012-68185013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11706410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11708116	0.86[ASN][1000 genomes]
rs11709861	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12486136	0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12486933	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13076275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs13085443	0.86[ASN][1000 genomes]
rs13085628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1583659	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs4129248	0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4130988	0.83[ASN][1000 genomes]
rs4130989	0.85[ASN][1000 genomes]
rs4130990	0.83[ASN][1000 genomes]
rs6419759	0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs6548962	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6548980	0.94[ASN][1000 genomes]
rs6548981	0.94[ASN][1000 genomes]
rs6548984	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[YRI][hapmap];0.94[ASN][1000 genomes]
rs6548985	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6548999	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6549020	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6774687	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7428056	0.88[GIH][hapmap]
rs7428837	0.85[ASN][1000 genomes]
rs7429303	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs7430480	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430568	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7433022	0.83[ASN][1000 genomes]
rs7433028	0.86[ASN][1000 genomes]
rs7617661	0.89[ASW][hapmap];0.80[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.80[AMR][1000 genomes]
rs7638117	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815465	0.83[ASN][1000 genomes]
rs9819989	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs9820035	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9867661	0.90[GIH][hapmap]
rs9868432	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870065	0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002010	chr3:67785913-68312064	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1009871	chr3:67862617-68312064	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv536583	chr3:67862617-68312064	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv999747	chr3:68066423-68188180	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536584	chr3:68066423-68188180	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2752014	chr3:68091879-68416989	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1007450	chr3:68094416-68346546	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv876925	chr3:68180422-68288626	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6768632	LRIG1	cis	cerebellum	SCAN
rs6768632	FAM19A1	cis	cerebellum	SCAN
rs6768632	FRMD4B	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:68180800-68185400	Weak transcription	Fetal Brain Female	brain
2	chr3:68183800-68186000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr3:68183800-68186000	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr3:68184000-68186000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:68184000-68186000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:68184000-68186200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr3:68184200-68186200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:68184400-68186000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:68184600-68185400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:68184600-68185600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:68184800-68185800	Enhancers	Fetal Brain Male	brain
12	chr3:68185000-68185400	Weak transcription	H1 Cell Line	embryonic stem cell

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