Variant report

Variant	rs2592948
Chromosome Location	chr4:129994690-129994691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129993871..129996634-chr4:130011774..130013975,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10028974	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11098994	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12503465	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs12504200	0.81[YRI][hapmap]
rs12512345	0.81[YRI][hapmap]
rs1376202	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap]
rs172168	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17416188	0.81[YRI][hapmap]
rs17416706	0.82[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1756011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1757926	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757929	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757936	0.82[JPT][hapmap]
rs1757937	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1757938	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1757942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1838911	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs189236	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1900397	0.81[YRI][hapmap]
rs2044523	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2118045	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2597837	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2655311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777822	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2777823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280596	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs280597	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280601	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3099902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3099903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3113488	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3113490	0.80[JPT][hapmap]
rs337276	0.84[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs337279	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3980331	0.81[AFR][1000 genomes]
rs4975294	0.81[YRI][hapmap]
rs55865936	0.89[ASN][1000 genomes]
rs62316971	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62316978	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6845314	0.81[AFR][1000 genomes]
rs6847784	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs72685321	0.81[AFR][1000 genomes]
rs7654405	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671508	0.82[JPT][hapmap]
rs789982	0.82[JPT][hapmap]
rs796886	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2592948	C4orf33	cis	Artery Tibial	GTEx
rs2592948	C4orf33	cis	parietal	SCAN
rs2592948	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs2592948	C4orf33	cis	lymphoblastoid	seeQTL
rs2592948	SCLT1	cis	cerebellum	SCAN
rs2592948	LOC132321	cis	normal skin	skin_eQTL

Chromatin state (count:97 , 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	chr4:129983000-130001600	Weak transcription	Fetal Heart	heart
3	chr4:129985000-130000000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:129985000-130000000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:129985000-130000000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:129985000-130000200	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:129985200-129997200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:129985200-129999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:129985200-130000000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:129985200-130000000	Weak transcription	Fetal Stomach	stomach
11	chr4:129985200-130000200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:129985200-130000600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:129985200-130000600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:129985200-130000600	Weak transcription	Adipose Nuclei	Adipose
15	chr4:129985200-130000600	Weak transcription	Placenta	Placenta
16	chr4:129985200-130000600	Weak transcription	Gastric	stomach
17	chr4:129985200-130000600	Weak transcription	Lung	lung
18	chr4:129985200-130000600	Weak transcription	Ovary	ovary
19	chr4:129985200-130000600	Weak transcription	Spleen	Spleen
20	chr4:129985200-130001000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:129985200-130001200	Weak transcription	Small Intestine	intestine
22	chr4:129985200-130002200	Weak transcription	Pancreas	Pancrea
23	chr4:129985200-130012200	Weak transcription	HSMM	muscle
24	chr4:129985200-130013000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:129985200-130013200	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:129986600-130000800	Weak transcription	Osteobl	bone
27	chr4:129986600-130001000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:129987000-130011600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:129987400-130000600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:129987600-130000600	Weak transcription	NHLF	lung
31	chr4:129990400-130004000	Weak transcription	Right Ventricle	heart
32	chr4:129990800-129996800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr4:129991600-129998600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:129991600-130011800	Weak transcription	Hela-S3	cervix
35	chr4:129991800-130012000	Weak transcription	HUVEC	blood vessel
36	chr4:129992000-130000200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:129992200-130000600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:129992200-130003600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:129992200-130005400	Weak transcription	Psoas Muscle	Psoas
40	chr4:129992400-130001200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:129992600-129994800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:129992600-130000800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:129992600-130005800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:129992600-130012000	Weak transcription	HepG2	liver
45	chr4:129992800-130001000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:129993000-129997800	ZNF genes & repeats	GM12878-XiMat	blood
47	chr4:129993000-130007600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:129993000-130012000	Weak transcription	Stomach Mucosa	stomach
49	chr4:129993200-129994800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr4:129993200-129995000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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