Variant report

Variant	rs1699384
Chromosome Location	chr4:129987071-129987072
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10002332	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10032000	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs1030831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1037147	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12171333	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13109003	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130762	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1374491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596963	0.87[ASN][1000 genomes]
rs1668289	0.94[CEU][hapmap];0.86[JPT][hapmap]
rs1699379	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699380	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1699385	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699387	0.93[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1699388	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699389	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699394	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17014265	0.89[CHB][hapmap]
rs1709419	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1756012	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]
rs1757924	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757927	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757928	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757930	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757936	0.84[AMR][1000 genomes]
rs1854773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1854774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs189235	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2034498	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2083634	1.00[CEU][hapmap]
rs2198042	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2597836	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2655310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs280603	1.00[CEU][hapmap];0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs280604	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3105369	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113407	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs3113489	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113490	0.84[AMR][1000 genomes]
rs318502	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs318503	0.84[JPT][hapmap]
rs318536	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs318543	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs318552	0.94[CEU][hapmap];0.86[JPT][hapmap]
rs337263	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs337270	0.94[EUR][1000 genomes]
rs337275	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs337277	0.93[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337278	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35006492	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs389376	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs390260	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs391396	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs395864	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs426521	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4394010	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs445294	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4466058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474667	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs474794	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs487233	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs487501	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4975193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975194	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517659	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57501568	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs576492	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58689608	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6534707	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66921209	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7655841	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7671508	0.84[AMR][1000 genomes]
rs789982	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1699384	C4orf33	cis	Whole Blood	GTEx
rs1699384	C4orf33	cis	multi-tissue	Pritchard
rs1699384	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs1699384	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs1699384	C4orf33	cis	Adipose Subcutaneous	GTEx
rs1699384	LOC132321	cis	normal skin	skin_eQTL
rs1699384	C4orf33	cis	Artery Tibial	GTEx
rs1699384	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129977200-130000600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:129981200-129987200	ZNF genes & repeats	Dnd41	blood
3	chr4:129983000-129994000	Weak transcription	Fetal Kidney	kidney
4	chr4:129983000-130001600	Weak transcription	Fetal Heart	heart
5	chr4:129985000-129991800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:129985000-130000000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:129985000-130000000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:129985000-130000000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:129985000-130000200	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:129985200-129988800	Weak transcription	Aorta	Aorta
11	chr4:129985200-129990000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:129985200-129992800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:129985200-129993800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:129985200-129993800	Weak transcription	Fetal Thymus	thymus
15	chr4:129985200-129993800	Weak transcription	Thymus	Thymus
16	chr4:129985200-129994000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:129985200-129994000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:129985200-129994000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:129985200-129994000	Weak transcription	Left Ventricle	heart
20	chr4:129985200-129994000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:129985200-129994000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:129985200-129994200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:129985200-129994200	Weak transcription	Esophagus	oesophagus
24	chr4:129985200-129994200	Weak transcription	K562	blood
25	chr4:129985200-129997200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:129985200-129999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:129985200-130000000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:129985200-130000000	Weak transcription	Fetal Stomach	stomach
29	chr4:129985200-130000200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:129985200-130000600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:129985200-130000600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:129985200-130000600	Weak transcription	Adipose Nuclei	Adipose
33	chr4:129985200-130000600	Weak transcription	Placenta	Placenta
34	chr4:129985200-130000600	Weak transcription	Gastric	stomach
35	chr4:129985200-130000600	Weak transcription	Lung	lung
36	chr4:129985200-130000600	Weak transcription	Ovary	ovary
37	chr4:129985200-130000600	Weak transcription	Spleen	Spleen
38	chr4:129985200-130001000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:129985200-130001200	Weak transcription	Small Intestine	intestine
40	chr4:129985200-130002200	Weak transcription	Pancreas	Pancrea
41	chr4:129985200-130012200	Weak transcription	HSMM	muscle
42	chr4:129985200-130013000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr4:129985200-130013200	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:129985400-129987200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:129985400-129988600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr4:129985400-129993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:129985600-129993200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:129985800-129987600	Enhancers	NHLF	lung
49	chr4:129986000-129988800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:129986000-129989000	Weak transcription	Primary B cells from cord blood	blood

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