Variant report

Variant	rs2293374
Chromosome Location	chr3:133547245-133547246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133534500..133536189-chr3:133546223..133548378,2	K562	blood:
2	chr3:133539699..133541216-chr3:133545754..133547424,2	K562	blood:
3	chr3:133544073..133548736-chr3:133549293..133553405,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRPRB-1	chr3:133546682-133547693	NONHSAT092207

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1043147	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12487258	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs12637730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358024	1.00[LWK][hapmap]
rs16840994	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16841004	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2249322	0.84[JPT][hapmap]
rs2293373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293375	0.92[GIH][hapmap];0.84[MEX][hapmap]
rs2692667	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2692668	0.88[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs2692670	0.84[JPT][hapmap]
rs2715607	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2715608	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2715609	0.84[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3811659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs57847564	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58851383	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6773354	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7626433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2293374	SRPRB	Cis_1M	lymphoblastoid	RTeQTL
rs2293374	RAB6B	cis	parietal	SCAN
rs2293374	SRPRB	cis	uninvolved skin	skin_eQTL
rs2293374	SRPRB	cis	multi-tissue	Pritchard
rs2293374	SRPRB	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133539400-133572200	Weak transcription	Fetal Brain Male	brain
2	chr3:133540800-133547600	Weak transcription	Fetal Heart	heart
3	chr3:133541000-133551000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:133541400-133558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:133541400-133559600	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:133541600-133547400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:133541600-133547400	Weak transcription	Hela-S3	cervix
8	chr3:133542000-133547400	Weak transcription	HepG2	liver
9	chr3:133542000-133547600	Weak transcription	NHLF	lung
10	chr3:133542000-133555400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:133542000-133563600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:133542600-133557800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:133542800-133569000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:133543000-133553600	Weak transcription	Fetal Lung	lung
15	chr3:133543200-133547600	Weak transcription	K562	blood
16	chr3:133543400-133560600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:133543600-133548000	Weak transcription	Fetal Intestine Large	intestine
18	chr3:133543600-133548800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:133543600-133549200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:133543600-133550400	Weak transcription	Thymus	Thymus
21	chr3:133543800-133548400	Weak transcription	HSMMtube	muscle
22	chr3:133543800-133550800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:133543800-133552400	Weak transcription	Placenta	Placenta
24	chr3:133543800-133554000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:133543800-133560000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:133544000-133547600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:133544000-133550600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:133544000-133556600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:133544200-133549800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:133544200-133551600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:133544200-133551600	Weak transcription	Aorta	Aorta
32	chr3:133544200-133557600	Weak transcription	Adipose Nuclei	Adipose
33	chr3:133544400-133547600	Weak transcription	Right Ventricle	heart
34	chr3:133544400-133547800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:133544400-133559800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:133544600-133562200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:133544600-133573200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:133544600-133584200	Weak transcription	Esophagus	oesophagus
39	chr3:133544800-133547400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:133544800-133547400	Weak transcription	Ovary	ovary
41	chr3:133544800-133547600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:133544800-133547600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:133544800-133547800	Weak transcription	Lung	lung
44	chr3:133545000-133547600	Weak transcription	Left Ventricle	heart
45	chr3:133545000-133547800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:133545000-133582800	Weak transcription	Gastric	stomach
47	chr3:133545200-133547600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:133545200-133548200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:133545200-133550400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:133545200-133552400	Weak transcription	Spleen	Spleen

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