Variant report

Variant	rs389376
Chromosome Location	chr4:130036179-130036180
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:130030784..130034303-chr4:130034493..130036505,5	K562	blood:
2	chr4:130028612..130032885-chr4:130034533..130038076,4	K562	blood:
3	chr4:130013027..130015961-chr4:130034387..130037215,2	MCF-7	breast:
4	chr4:130036050..130038012-chr4:130049891..130052657,2	K562	blood:

Variant related genes	Relation type
ENSG00000151466	Chromatin interaction
ENSG00000151470	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10002332	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs10032000	0.87[CEU][hapmap]
rs1030831	0.93[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1037147	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12171333	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs13109003	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13130762	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1374491	0.93[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699379	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699380	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699384	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1699385	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699387	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1699388	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699389	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699391	0.93[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699393	0.93[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1699394	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17014265	0.89[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1709419	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1709422	0.89[YRI][hapmap]
rs17185550	0.86[YRI][hapmap]
rs1756012	0.93[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1757924	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757925	0.93[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757927	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757928	0.87[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757930	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757935	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757936	0.81[LWK][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs1854773	0.93[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1854774	0.93[CEU][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs189235	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	0.93[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.86[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];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs3105369	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3113489	0.87[CEU][hapmap];0.82[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3113490	0.83[AMR][1000 genomes]
rs318543	0.87[CEU][hapmap]
rs318552	0.87[CEU][hapmap]
rs337263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs337270	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337275	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs337277	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs337278	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35006492	0.92[EUR][1000 genomes]
rs390260	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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395864	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs426521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[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]
rs4394010	0.92[EUR][1000 genomes]
rs445294	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4466058	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs474667	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs474794	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs487233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975193	0.89[ASW][hapmap];0.93[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4975194	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs517659	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57501568	0.93[EUR][1000 genomes]
rs576492	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58689608	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6534707	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66921209	0.90[EUR][1000 genomes]
rs7655841	0.93[CEU][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs7671508	0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs789982	0.83[AMR][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
rs389376	C4orf33	cis	cerebellum	SCAN
rs389376	C4orf33	cis	lymphoblastoid	seeQTL
rs389376	C4orf33	cis	Artery Tibial	GTEx
rs389376	LOC132321	cis	multi-tissue	Pritchard
rs389376	C4orf33	cis	parietal	SCAN
rs389376	C4orf33	cis	Lymphoblastoid	GTEx
rs389376	LOC132321	cis	normal skin	skin_eQTL
rs389376	C4orf33	cis	Adipose Subcutaneous	GTEx
rs389376	C4orf33	cis	multi-tissue	Pritchard
rs389376	C4orf33	cis	Whole Blood	GTEx
rs389376	SCLT1	cis	cerebellum	SCAN
rs389376	ZNF226	trans	cerebellum	SCAN

Chromatin state (count:25 , 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	chr4:130032400-130036400	Weak transcription	Fetal Heart	heart
15	chr4:130032400-130037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:130032400-130038000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:130032400-130038200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:130032400-130040000	Weak transcription	Primary T cells from cord blood	blood
19	chr4:130032400-130052200	Weak transcription	Aorta	Aorta
20	chr4:130033400-130036800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr4:130033600-130036800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:130034000-130036800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:130034800-130038400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:130035800-130036200	Strong transcription	Left Ventricle	heart
25	chr4:130036000-130044600	Weak transcription	Pancreas	Pancrea

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