Variant report

Variant	rs353547
Chromosome Location	chr3:52268866-52268867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52268502..52270036-chr3:52311908..52314756,2	K562	blood:
2	chr3:52264729..52268939-chr3:52269297..52274565,7	K562	blood:
3	chr3:52268721..52271141-chr3:52272963..52274697,2	K562	blood:
4	chr3:52268278..52270898-chr3:52320244..52322252,2	K562	blood:
5	chr3:52237538..52239205-chr3:52267167..52269344,2	K562	blood:
6	chr3:52257505..52260127-chr3:52268132..52270399,2	K562	blood:

Variant related genes	Relation type
ENSG00000164091	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000239732	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1060330	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11717383	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs13094687	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs164640	0.81[CHB][hapmap]
rs181274	0.81[CHB][hapmap]
rs187084	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2267847	0.88[ASN][1000 genomes]
rs2272088	0.81[JPT][hapmap]
rs2276834	0.86[ASN][1000 genomes]
rs34228726	0.85[ASN][1000 genomes]
rs34569561	0.85[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs352139	0.81[CHB][hapmap]
rs352140	0.81[CHB][hapmap]
rs352158	0.81[CHB][hapmap]
rs352162	0.81[CHB][hapmap]
rs352163	0.81[CHB][hapmap]
rs352165	0.81[CHB][hapmap]
rs352166	0.81[CHB][hapmap]
rs352167	0.81[CHB][hapmap]
rs352168	0.81[CHB][hapmap]
rs352169	0.81[CHB][hapmap]
rs352170	0.81[CHB][hapmap]
rs352171	0.81[CHB][hapmap]
rs3844291	0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs3852063	0.86[ASN][1000 genomes]
rs3852064	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs411457	0.86[CHB][hapmap]
rs524986	0.81[CHB][hapmap]
rs57615517	0.85[ASN][1000 genomes]
rs57630131	0.84[ASN][1000 genomes]
rs59565798	0.86[ASN][1000 genomes]
rs610060	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs614288	0.81[CHB][hapmap]
rs6445358	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs730050	0.81[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7614727	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7618915	0.85[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7622851	0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7629072	0.88[ASN][1000 genomes]
rs9311474	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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 miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs353547	SPCS1	cis	parietal	SCAN
rs353547	GNL3	cis	parietal	SCAN
rs353547	PPM1M	cis	cerebellum	SCAN
rs353547	FLJ12442	cis	multi-tissue	Pritchard
rs353547	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs353547	NT5DC2	cis	parietal	SCAN
rs353547	RBM6	cis	cerebellum	SCAN
rs353547	SEMA3G	cis	parietal	SCAN
rs353547	ITIH4	cis	parietal	SCAN
rs353547	PPM1M	cis	Artery Tibial	GTEx
rs353547	NT5DC2	cis	lymphoblastoid	seeQTL
rs353547	NEK4	cis	parietal	SCAN
rs353547	GNL3	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:52253200-52269600	Weak transcription	Fetal Kidney	kidney
3	chr3:52255200-52270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:52261000-52269400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:52261200-52270800	Strong transcription	Fetal Stomach	stomach
6	chr3:52261400-52269000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:52261400-52269600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:52261600-52269800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr3:52261600-52270000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:52261600-52270000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:52261600-52270600	Strong transcription	NHEK	skin
12	chr3:52261800-52269400	Strong transcription	Brain Germinal Matrix	brain
13	chr3:52261800-52269800	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr3:52261800-52269800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:52261800-52270000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:52261800-52270800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:52262000-52269200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:52262400-52269800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:52262400-52269800	Strong transcription	Osteobl	bone
20	chr3:52262400-52270000	Strong transcription	NHLF	lung
21	chr3:52263000-52269800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:52263200-52269000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:52264200-52271400	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr3:52264600-52270000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr3:52264800-52270600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:52265000-52269400	Weak transcription	Hela-S3	cervix
27	chr3:52265000-52270400	Weak transcription	K562	blood
28	chr3:52265000-52272000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:52265200-52269400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr3:52265200-52270400	Weak transcription	HSMMtube	muscle
31	chr3:52265200-52270800	Weak transcription	HUVEC	blood vessel
32	chr3:52265400-52269200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:52265400-52269200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:52265400-52269600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:52265400-52269800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr3:52265400-52270800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:52265400-52271800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:52265600-52269600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:52265600-52270400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:52265600-52270400	Weak transcription	Brain Substantia Nigra	brain
41	chr3:52265600-52270400	Strong transcription	Fetal Intestine Small	intestine
42	chr3:52265600-52270400	Weak transcription	Stomach Mucosa	stomach
43	chr3:52265600-52270400	Weak transcription	HMEC	breast
44	chr3:52265600-52270600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:52265600-52270600	Weak transcription	Small Intestine	intestine
46	chr3:52265600-52270800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:52265600-52270800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:52265600-52271200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:52265800-52270000	Genic enhancers	Primary T cells from cord blood	blood
50	chr3:52265800-52270000	Genic enhancers	Monocytes-CD14+_RO01746	blood

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