Variant report

Variant	rs390260
Chromosome Location	chr4:130036591-130036592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:130028612..130032885-chr4:130034533..130038076,4	K562	blood:
2	chr4:130013027..130015961-chr4:130034387..130037215,2	MCF-7	breast:
3	chr4:130036050..130038012-chr4:130049891..130052657,2	K562	blood:

Variant related genes	Relation type
ENSG00000151470	Chromatin interaction
ENSG00000151466	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10002332	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs10032000	0.87[CEU][hapmap]
rs1030831	0.94[ASW][hapmap];0.93[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1037147	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12171333	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs13109003	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13130762	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1374491	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699379	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1699384	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1699385	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699387	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699388	0.93[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699389	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699391	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699393	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699394	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17014265	0.89[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs1709419	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1756012	0.93[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757924	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757925	0.88[ASW][hapmap];0.93[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757927	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757928	0.87[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757930	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757935	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1854773	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1854774	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs189235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034498	0.90[EUR][1000 genomes]
rs2083634	0.93[CEU][hapmap]
rs2198042	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs2597836	0.87[EUR][1000 genomes]
rs2655310	0.94[ASW][hapmap];0.93[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs280603	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs280604	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs3099899	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs3105369	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3113489	0.87[CEU][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs318552	0.87[CEU][hapmap]
rs337263	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337270	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337275	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs337276	0.84[YRI][hapmap]
rs337277	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs337278	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35006492	0.92[EUR][1000 genomes]
rs389376	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs391396	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs395864	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs426521	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394010	0.92[EUR][1000 genomes]
rs445294	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4466058	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs474667	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474794	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487233	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs487501	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975193	0.82[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4975194	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs517659	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57501568	0.93[EUR][1000 genomes]
rs576492	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58689608	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6534707	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66921209	0.90[EUR][1000 genomes]
rs7655841	0.93[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs390260	LOC132321	cis	normal skin	skin_eQTL
rs390260	LOC132321	cis	multi-tissue	Pritchard
rs390260	C4orf33	cis	multi-tissue	Pritchard
rs390260	C4orf33	cis	lymphoblastoid	seeQTL
rs390260	C4orf33	cis	Whole Blood	GTEx
rs390260	C4orf33	cis	Adipose Subcutaneous	GTEx
rs390260	C4orf33	cis	Artery Tibial	GTEx
rs390260	C4orf33	cis	parietal	SCAN
rs390260	C4orf33	cis	cerebellum	SCAN
rs390260	ZNF226	trans	cerebellum	SCAN
rs390260	C4orf33	cis	Lymphoblastoid	GTEx
rs390260	SCLT1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130017600-130040400	Weak transcription	Lung	lung
2	chr4:130018000-130038000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:130028800-130036600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:130029200-130040000	Weak transcription	Esophagus	oesophagus
5	chr4:130029400-130041200	Weak transcription	Spleen	Spleen
6	chr4:130029600-130038600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:130031400-130036800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr4:130031800-130036800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:130031800-130037400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:130031800-130037400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:130031800-130039800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:130031800-130040000	Weak transcription	Dnd41	blood
13	chr4:130032000-130037400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:130032400-130037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:130032400-130038000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:130032400-130038200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:130032400-130040000	Weak transcription	Primary T cells from cord blood	blood
18	chr4:130032400-130052200	Weak transcription	Aorta	Aorta
19	chr4:130033400-130036800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr4:130033600-130036800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:130034000-130036800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:130034800-130038400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:130036000-130044600	Weak transcription	Pancreas	Pancrea
24	chr4:130036200-130037800	Weak transcription	Left Ventricle	heart

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