Variant report

Variant	rs2131108
Chromosome Location	chr3:49665390-49665391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49664437..49667415-chr3:49710388..49712286,2	K562	blood:
2	chr3:49663002..49665854-chr3:49667591..49669452,2	K562	blood:
3	chr3:49664354..49666202-chr3:49667591..49669147,2	K562	blood:

Variant related genes	Relation type
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10452032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	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];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130207	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130208	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	0.94[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130217	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11709734	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs11720705	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs11721148	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12583	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs12637313	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13096480	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs1352889	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463728	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs1491985	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1532204	0.94[CEU][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1586827	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	0.82[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs2029591	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs2312462	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs2329021	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];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs34890793	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs3866330	0.92[MKK][hapmap]
rs3905330	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs4241405	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs4855833	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855845	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	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];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855882	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754265	0.81[EUR][1000 genomes]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs62262671	0.81[EUR][1000 genomes]
rs62262672	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262673	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262675	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446284	0.84[AMR][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs6446286	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6797299	0.94[CEU][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805609	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6809879	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7613603	1.00[CEU][hapmap]
rs7620848	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7628207	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs7637711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs7653505	1.00[CHD][hapmap];0.86[MKK][hapmap]
rs8897	1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9830730	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9849038	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9860055	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9862534	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs9870755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9870858	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9871024	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883000	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2131108	QRICH1	cis	cerebellum	SCAN
rs2131108	DALRD3	cis	cerebellum	SCAN
rs2131108	AMT	cis	Thyroid	GTEx
rs2131108	AMT	cis	parietal	SCAN
rs2131108	AMT	cis	lymphoblastoid	seeQTL
rs2131108	P4HTM	cis	parietal	SCAN
rs2131108	RNF123	cis	parietal	SCAN
rs2131108	NICN1	cis	multi-tissue	Pritchard
rs2131108	GNL3	cis	cerebellum	SCAN
rs2131108	AMT	cis	lung	GTEx
rs2131108	GMPPB	cis	parietal	SCAN
rs2131108	AMT	cis	multi-tissue	Pritchard
rs2131108	OR9G4	trans	parietal	SCAN
rs2131108	ZNF589	cis	parietal	SCAN
rs2131108	DALRD3	cis	parietal	SCAN
rs2131108	RNF123	cis	Artery Tibial	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49654400-49668200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:49655000-49668800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:49655600-49676200	Weak transcription	HepG2	liver
4	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:49660800-49682600	Weak transcription	Liver	Liver
6	chr3:49661000-49669200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:49661600-49692400	Weak transcription	Ovary	ovary
8	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
9	chr3:49662000-49667600	Strong transcription	Brain Germinal Matrix	brain
10	chr3:49662200-49666800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:49662400-49665800	Strong transcription	Fetal Brain Female	brain
12	chr3:49662600-49668600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:49662800-49668400	Weak transcription	Lung	lung
14	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
15	chr3:49663600-49665400	Weak transcription	Brain Angular Gyrus	brain
16	chr3:49663600-49667000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:49663800-49679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:49664200-49668200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:49664200-49669000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
21	chr3:49664400-49668200	Weak transcription	NH-A	brain
22	chr3:49664600-49667800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:49664600-49674000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:49664600-49680000	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:49665000-49672400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:49665200-49665400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:49665200-49667000	Weak transcription	Brain Anterior Caudate	brain
28	chr3:49665200-49668800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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