Variant report

Variant	rs189235
Chromosome Location	chr4:130035370-130035371
allele	A/T
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:

Variant related genes	Relation type
ENSG00000151466	Chromatin interaction
ENSG00000151470	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10002332	0.92[EUR][1000 genomes]
rs1030831	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1037147	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12171333	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	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699379	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699380	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1699384	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1699385	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699387	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699388	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699389	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699391	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699393	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699394	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17014265	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	0.82[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	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757927	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757928	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757930	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1757935	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1854773	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1854774	0.83[EUR][1000 genomes]
rs2034498	0.90[EUR][1000 genomes]
rs2198042	0.94[EUR][1000 genomes]
rs2597836	0.87[EUR][1000 genomes]
rs2655310	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs280603	0.94[EUR][1000 genomes]
rs280604	0.92[EUR][1000 genomes]
rs3099899	0.94[EUR][1000 genomes]
rs3105369	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3113489	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs337263	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]
rs337277	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	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs426521	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	0.94[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	0.85[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	0.94[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs189235	C4orf33	cis	Artery Tibial	GTEx
rs189235	C4orf33	cis	multi-tissue	Pritchard
rs189235	C4orf33	cis	Adipose Subcutaneous	GTEx
rs189235	C4orf33	cis	Whole Blood	GTEx
rs189235	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs189235	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs189235	C4orf33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 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	chr4:130029400-130035400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:130029400-130041200	Weak transcription	Spleen	Spleen
7	chr4:130029600-130038600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:130030800-130035600	Weak transcription	Gastric	stomach
9	chr4:130031400-130036800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:130031800-130035800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:130031800-130035800	Weak transcription	Left Ventricle	heart
12	chr4:130031800-130036800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:130031800-130037400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:130031800-130037400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:130031800-130039800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:130031800-130040000	Weak transcription	Dnd41	blood
17	chr4:130032000-130035400	Weak transcription	Ovary	ovary
18	chr4:130032000-130037400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:130032400-130036400	Weak transcription	Fetal Heart	heart
20	chr4:130032400-130037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:130032400-130038000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:130032400-130038200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:130032400-130040000	Weak transcription	Primary T cells from cord blood	blood
24	chr4:130032400-130052200	Weak transcription	Aorta	Aorta
25	chr4:130033400-130036800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:130033600-130036800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:130034000-130036800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:130034600-130035400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr4:130034800-130038400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:130035000-130035400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr4:130035000-130035400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:130035200-130036000	Enhancers	Pancreas	Pancrea

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