Variant report

Variant	rs1699388
Chromosome Location	chr4:130003237-130003238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10002332	1.00[CEU][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10032000	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs1030831	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1037147	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12171333	1.00[CEU][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13109003	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13130762	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1374491	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1596963	0.85[ASN][1000 genomes]
rs1668289	0.94[CEU][hapmap];0.86[JPT][hapmap]
rs1699379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699380	0.93[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699384	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]
rs1699385	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699387	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699391	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699393	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1699394	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1709419	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1709422	0.84[YRI][hapmap]
rs1756012	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]
rs1757924	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757925	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757927	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757928	0.93[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757930	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1757935	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1757936	0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs1854773	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854774	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs189235	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2034498	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2083634	1.00[CEU][hapmap]
rs2198042	1.00[CEU][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2597836	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2655310	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs280594	0.81[YRI][hapmap]
rs280603	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs280604	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3099899	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3105369	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3113407	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs3113489	0.93[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113490	0.80[YRI][hapmap];0.88[AMR][1000 genomes]
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];0.89[CHB][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs337270	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337275	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337277	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337278	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35006492	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs389376	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]
rs390260	0.93[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs391396	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs395864	0.94[CEU][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs426521	0.93[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4394010	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs445294	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4466058	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs474667	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs474794	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs487233	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs487501	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4975193	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975194	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs517659	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57501568	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs576492	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58689608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534707	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66921209	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7655841	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7671508	0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs789982	0.88[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1699388	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs1699388	LOC132321	cis	normal skin	skin_eQTL
rs1699388	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs1699388	C4orf33	cis	Whole Blood	GTEx
rs1699388	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs1699388	C4orf33	cis	multi-tissue	Pritchard
rs1699388	C4orf33	cis	Lymphoblastoid	GTEx
rs1699388	C4orf33	cis	Artery Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

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	chr4:129987000-130011600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:129990400-130004000	Weak transcription	Right Ventricle	heart
6	chr4:129991600-130011800	Weak transcription	Hela-S3	cervix
7	chr4:129991800-130012000	Weak transcription	HUVEC	blood vessel
8	chr4:129992200-130003600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:129992200-130005400	Weak transcription	Psoas Muscle	Psoas
10	chr4:129992600-130005800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:129992600-130012000	Weak transcription	HepG2	liver
12	chr4:129993000-130007600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:129993000-130012000	Weak transcription	Stomach Mucosa	stomach
14	chr4:129995600-130011400	Weak transcription	A549	lung
15	chr4:129997200-130012000	Weak transcription	NHEK	skin
16	chr4:129997600-130010000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:129999000-130003400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:129999000-130008200	ZNF genes & repeats	GM12878-XiMat	blood
19	chr4:129999200-130006400	Weak transcription	Fetal Kidney	kidney
20	chr4:129999200-130012600	Weak transcription	NH-A	brain
21	chr4:129999400-130005400	Weak transcription	Brain Substantia Nigra	brain
22	chr4:129999400-130011400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:129999800-130003400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:130000000-130003600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:130000200-130011400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:130000400-130013000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:130001200-130003600	Strong transcription	Fetal Thymus	thymus
28	chr4:130001400-130011200	Weak transcription	NHLF	lung
29	chr4:130001400-130013000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:130001800-130003400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:130001800-130003600	Strong transcription	Primary B cells from cord blood	blood
32	chr4:130001800-130007600	Weak transcription	Small Intestine	intestine
33	chr4:130001800-130011200	Weak transcription	Fetal Heart	heart
34	chr4:130001800-130012000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:130001800-130013000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:130002000-130011800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:130002000-130012600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr4:130002000-130013200	Weak transcription	Brain Angular Gyrus	brain
39	chr4:130002200-130012000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:130002200-130013400	Weak transcription	Placenta	Placenta
41	chr4:130002600-130005400	Weak transcription	Brain Hippocampus Middle	brain
42	chr4:130002600-130006800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:130002600-130009600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr4:130002600-130011400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr4:130002600-130012200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:130002800-130003400	Strong transcription	K562	blood
47	chr4:130002800-130003600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr4:130002800-130003600	Strong transcription	NHDF-Ad	bronchial
49	chr4:130002800-130004000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr4:130002800-130004200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links