Variant report

Variant	rs1756012
Chromosome Location	chr4:130018971-130018972
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	MAFK	chr4:130018605-130019003	K562	blood:	n/a	n/a
2	IRF1	chr4:130018382-130019197	K562	blood:	n/a	n/a
3	CUX1	chr4:130018720-130019090	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:130017343..130020226-chr4:130031173..130032927,2	K562	blood:

Variant related genes	Relation type
SCLT1	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10002332	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10032000	0.93[CEU][hapmap]
rs1030831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1037147	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12171333	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13109003	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13130762	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1374491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1596963	0.80[ASN][1000 genomes]
rs1668289	0.94[CEU][hapmap]
rs1699379	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699380	0.93[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1699384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699385	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699387	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1699388	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699389	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699394	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014265	0.89[CHB][hapmap]
rs1709419	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757924	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757927	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757928	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757930	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1757935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757936	0.85[AMR][1000 genomes]
rs1854773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1854774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs189235	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2034498	0.90[EUR][1000 genomes]
rs2083634	1.00[CEU][hapmap]
rs2198042	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2597836	0.88[EUR][1000 genomes]
rs2655310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs280603	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs280604	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3099899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3105369	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3113407	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs3113489	0.93[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3113490	0.85[AMR][1000 genomes]
rs318536	0.93[CEU][hapmap]
rs318543	0.93[CEU][hapmap]
rs318552	0.94[CEU][hapmap]
rs337263	0.93[CEU][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs337270	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337275	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337277	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs337278	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35006492	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs389376	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]
rs390260	0.93[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs391396	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs395864	0.94[CEU][hapmap];0.89[CHB][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs426521	0.93[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4394010	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs445294	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4466058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs474667	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs474794	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs487233	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs487501	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4975193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975194	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs517659	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57501568	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs576492	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58689608	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6534707	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66921209	0.91[EUR][1000 genomes]
rs7655841	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[EUR][1000 genomes]
rs7671508	0.85[AMR][1000 genomes]
rs789982	0.85[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1756012	C4orf33	cis	Artery Tibial	GTEx
rs1756012	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs1756012	C4orf33	cis	Lymphoblastoid	GTEx
rs1756012	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs1756012	LOC132321	cis	normal skin	skin_eQTL
rs1756012	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs1756012	C4orf33	cis	Adipose Subcutaneous	GTEx
rs1756012	C4orf33	cis	Whole Blood	GTEx
rs1756012	C4orf33	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130017200-130019200	Active TSS	GM12878-XiMat	blood
2	chr4:130017600-130024600	Weak transcription	Fetal Brain Male	brain
3	chr4:130017600-130031400	Weak transcription	Pancreas	Pancrea
4	chr4:130017600-130031400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:130017600-130040400	Weak transcription	Lung	lung
6	chr4:130017800-130024200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:130017800-130026400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:130017800-130027200	Weak transcription	Small Intestine	intestine
9	chr4:130017800-130030800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:130017800-130031400	Weak transcription	Aorta	Aorta
11	chr4:130017800-130031400	Weak transcription	Left Ventricle	heart
12	chr4:130017800-130031400	Weak transcription	Ovary	ovary
13	chr4:130017800-130031400	Weak transcription	Right Ventricle	heart
14	chr4:130017800-130031600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:130017800-130032600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:130017800-130032800	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:130017800-130033400	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:130017800-130033400	Weak transcription	Thymus	Thymus
19	chr4:130017800-130034200	Weak transcription	Colonic Mucosa	Colon
20	chr4:130018000-130019600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:130018000-130019600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:130018000-130019800	Weak transcription	A549	lung
23	chr4:130018000-130021400	Weak transcription	Right Atrium	heart
24	chr4:130018000-130023600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr4:130018000-130023800	Weak transcription	Liver	Liver
26	chr4:130018000-130024400	Weak transcription	Placenta	Placenta
27	chr4:130018000-130024400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:130018000-130024600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:130018000-130024600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:130018000-130024600	Weak transcription	Fetal Lung	lung
31	chr4:130018000-130024800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:130018000-130024800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:130018000-130024800	Weak transcription	Adipose Nuclei	Adipose
34	chr4:130018000-130024800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:130018000-130025400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:130018000-130026400	Weak transcription	Fetal Kidney	kidney
37	chr4:130018000-130028000	Weak transcription	NH-A	brain
38	chr4:130018000-130030200	Weak transcription	Primary T cells from cord blood	blood
39	chr4:130018000-130030400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr4:130018000-130030600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:130018000-130031000	Weak transcription	Fetal Thymus	thymus
42	chr4:130018000-130031400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:130018000-130031400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:130018000-130031400	Weak transcription	Fetal Stomach	stomach
45	chr4:130018000-130032400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:130018000-130033000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:130018000-130033200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:130018000-130033400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr4:130018000-130034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:130018000-130038000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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