Variant report

Variant	rs1757936
Chromosome Location	chr4:130011891-130011892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:130011739-130015326	IMR90	lung:	n/a	n/a
2	POLR2A	chr4:130011530-130011980	MCF10A-Er-Src	breast:	n/a	n/a
3	WRNIP1	chr4:130011880-130012416	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:129731737..129733753-chr4:130010586..130013239,2	MCF-7	breast:
2	chr4:129993871..129996634-chr4:130011774..130013975,2	K562	blood:
3	chr4:130011776..130014103-chr4:130019273..130020805,2	K562	blood:
4	chr4:130003975..130008687-chr4:130008780..130012075,4	K562	blood:

Variant related genes	Relation type
C4orf33	TF binding region
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1030831	0.81[TSI][hapmap]
rs11934740	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13109003	0.87[AMR][1000 genomes]
rs1374491	0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs1699379	0.88[AMR][1000 genomes]
rs1699384	0.84[AMR][1000 genomes]
rs1699385	0.88[AMR][1000 genomes]
rs1699388	0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs1699389	0.88[AMR][1000 genomes]
rs1699391	0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs1699393	0.84[AMR][1000 genomes]
rs1699394	0.84[AMR][1000 genomes]
rs17185550	0.89[YRI][hapmap]
rs172168	0.82[JPT][hapmap]
rs1756012	0.85[AMR][1000 genomes]
rs1757925	0.81[TSI][hapmap]
rs1757928	0.81[TSI][hapmap]
rs1757930	0.84[AMR][1000 genomes]
rs1757938	0.82[JPT][hapmap]
rs1854773	0.85[YRI][hapmap];0.85[AMR][1000 genomes]
rs2592948	0.82[JPT][hapmap]
rs2655310	0.81[TSI][hapmap]
rs2655311	0.81[JPT][hapmap]
rs280594	0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs280595	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28711799	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099899	0.85[YRI][hapmap]
rs3099902	0.82[JPT][hapmap]
rs3099903	0.81[YRI][hapmap]
rs3113487	0.82[JPT][hapmap]
rs3113489	0.82[CHD][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs3113490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337263	0.81[LWK][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes]
rs337275	0.83[AMR][1000 genomes]
rs389376	0.81[LWK][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs391396	0.83[AMR][1000 genomes]
rs395864	0.83[AMR][1000 genomes]
rs487233	0.83[AMR][1000 genomes]
rs487501	0.83[AMR][1000 genomes]
rs4975193	0.82[CHD][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs4975194	0.88[AMR][1000 genomes]
rs517659	0.83[AMR][1000 genomes]
rs58689608	0.88[AMR][1000 genomes]
rs6534707	0.85[AMR][1000 genomes]
rs6812361	0.82[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6824219	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7655841	0.81[TSI][hapmap]
rs7671508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs789982	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1757936	C4orf33	cis	Lymphoblastoid	GTEx
rs1757936	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs1757936	LOC132321	cis	normal skin	skin_eQTL
rs1757936	C4orf33	cis	multi-tissue	Pritchard
rs1757936	C4orf33	cis	Artery Tibial	GTEx
rs1757936	C4orf33	cis	parietal	SCAN
rs1757936	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs1757936	SCLT1	cis	cerebellum	SCAN
rs1757936	C4orf33	cis	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129985200-130012200	Weak transcription	HSMM	muscle
2	chr4:129985200-130013000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:129985200-130013200	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:129991800-130012000	Weak transcription	HUVEC	blood vessel
5	chr4:129992600-130012000	Weak transcription	HepG2	liver
6	chr4:129993000-130012000	Weak transcription	Stomach Mucosa	stomach
7	chr4:129997200-130012000	Weak transcription	NHEK	skin
8	chr4:129999200-130012600	Weak transcription	NH-A	brain
9	chr4:130000400-130013000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:130001400-130013000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:130001800-130012000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:130001800-130013000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:130002000-130012600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:130002000-130013200	Weak transcription	Brain Angular Gyrus	brain
15	chr4:130002200-130012000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:130002200-130013400	Weak transcription	Placenta	Placenta
17	chr4:130002600-130012200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:130002800-130012000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:130002800-130012800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:130002800-130013000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:130002800-130013000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:130002800-130013000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:130002800-130013000	Weak transcription	Gastric	stomach
24	chr4:130002800-130013000	Weak transcription	Pancreas	Pancrea
25	chr4:130002800-130013000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:130002800-130013000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:130002800-130013200	Weak transcription	Aorta	Aorta
28	chr4:130002800-130013800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:130002800-130013800	Weak transcription	Ovary	ovary
30	chr4:130003000-130012000	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr4:130003000-130012000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:130003000-130012200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:130003000-130012200	Weak transcription	Fetal Stomach	stomach
34	chr4:130003000-130012200	Weak transcription	Osteobl	bone
35	chr4:130003000-130012600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:130003000-130012600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:130003000-130012600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:130003000-130012800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:130003000-130012800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:130003000-130013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:130003000-130013200	Weak transcription	Esophagus	oesophagus
42	chr4:130003600-130012200	Weak transcription	Fetal Thymus	thymus
43	chr4:130005000-130012200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:130005400-130012000	Weak transcription	NHDF-Ad	bronchial
45	chr4:130006800-130012200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:130007000-130012200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr4:130007000-130012400	Weak transcription	Fetal Lung	lung
48	chr4:130007000-130013000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:130007000-130013000	Weak transcription	Fetal Kidney	kidney
50	chr4:130007000-130013000	Weak transcription	Left Ventricle	heart

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