Variant report

Variant	rs2304442
Chromosome Location	chr3:49322027-49322028
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49313773..49316924-chr3:49320804..49323642,3	K562	blood:
2	chr3:49314878..49316924-chr3:49320804..49323442,2	K562	blood:

Variant related genes	Relation type
ENSG00000188315	Chromatin interaction
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10049462	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10865954	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11130184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11552724	1.00[JPT][hapmap]
rs11706189	1.00[JPT][hapmap]
rs11707940	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11713297	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11715581	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11719220	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11920267	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12490393	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12493001	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs12493284	0.97[ASN][1000 genomes]
rs12629637	0.83[ASN][1000 genomes]
rs12629759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12631989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12637576	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12715434	0.86[ASN][1000 genomes]
rs12715435	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13068038	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13077498	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13077723	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2117938	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2230929	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs34343820	0.86[ASN][1000 genomes]
rs34366700	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34514189	0.90[EUR][1000 genomes]
rs34566463	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap]
rs34567776	0.91[EUR][1000 genomes]
rs34915642	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35060561	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs35174559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35446411	0.90[EUR][1000 genomes]
rs35673421	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs35869135	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3774799	0.89[ASN][1000 genomes]
rs4279134	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4410472	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4513485	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4521268	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4955410	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4955418	1.00[JPT][hapmap]
rs4955419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4955420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4955432	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5030795	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs56038006	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6779394	1.00[JPT][hapmap]
rs67831908	0.86[ASN][1000 genomes]
rs6784111	1.00[JPT][hapmap]
rs67882627	0.90[EUR][1000 genomes]
rs73086105	0.81[AMR][1000 genomes]
rs7374375	0.90[ASN][1000 genomes]
rs7614738	0.80[ASN][1000 genomes]
rs7638154	0.84[ASN][1000 genomes]
rs7652746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9311439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9814987	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap]
rs9818758	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs9828310	0.86[ASN][1000 genomes]
rs9837237	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9837625	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9840050	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs9847839	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.86[ASN][1000 genomes]
rs9850917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9863142	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9864406	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9873994	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9874474	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880088	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9880309	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9883409	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990153	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[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	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv963481	chr3:49304260-49325571	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2304442	C3orf62	cis	parietal	SCAN
rs2304442	NICN1	cis	cerebellum	SCAN
rs2304442	GPX1	cis	parietal	SCAN
rs2304442	USP4	cis	multi-tissue	Pritchard
rs2304442	RNF123	cis	parietal	SCAN
rs2304442	NBEAL2	cis	cerebellum	SCAN
rs2304442	C3orf62	cis	cerebellum	SCAN
rs2304442	UQCRC1	cis	parietal	SCAN
rs2304442	CELSR3	cis	cerebellum	SCAN
rs2304442	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs2304442	NDUFAF3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49313200-49326200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49313200-49349400	Strong transcription	Dnd41	blood
4	chr3:49313600-49349200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:49314200-49324200	Strong transcription	Hela-S3	cervix
6	chr3:49314800-49334600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:49314800-49355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:49314800-49364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:49315200-49327600	Strong transcription	Placenta	Placenta
10	chr3:49315200-49349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:49315200-49349600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:49315200-49352600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
15	chr3:49315400-49327600	Strong transcription	GM12878-XiMat	blood
16	chr3:49315400-49335800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
18	chr3:49315600-49332400	Strong transcription	Brain Hippocampus Middle	brain
19	chr3:49315800-49333000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:49315800-49349200	Strong transcription	Fetal Brain Female	brain
21	chr3:49316200-49334600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:49316400-49328600	Strong transcription	Fetal Lung	lung
24	chr3:49316600-49340200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:49317000-49324200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:49317200-49334200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:49317200-49349400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
29	chr3:49317400-49331200	Strong transcription	Adipose Nuclei	Adipose
30	chr3:49317400-49332200	Strong transcription	Right Ventricle	heart
31	chr3:49317400-49334200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:49317400-49334200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr3:49317400-49334200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:49317400-49334200	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:49317400-49334200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:49317400-49334600	Strong transcription	Left Ventricle	heart
37	chr3:49317400-49349200	Strong transcription	Fetal Intestine Large	intestine
38	chr3:49317400-49349600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:49317600-49331600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:49318400-49322800	Weak transcription	K562	blood
43	chr3:49319200-49324200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:49319200-49333600	Strong transcription	HSMMtube	muscle
45	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:49319400-49333000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr3:49319400-49349600	Strong transcription	Liver	Liver
48	chr3:49319600-49323800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:49319600-49332600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:49319600-49334200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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