Variant report

Variant	rs6873548
Chromosome Location	chr5:147162565-147162566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr5:147161539-147162675	H1-neurons	neurons:	n/a	chr5:147162383-147162396 chr5:147162386-147162399
2	TAF1	chr5:147161491-147162677	H1-neurons	neurons:	n/a	n/a
3	ZNF143	chr5:147161994-147162586	H1-hESC	embryonic stem cell:	n/a	n/a
4	REST	chr5:147160061-147162882	H1-neurons	neurons:	n/a	chr5:147162383-147162396 chr5:147162386-147162399
5	CHD2	chr5:147161931-147162650	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr5:147162338-147162583	SK-N-SH_RA	brain:	n/a	n/a
7	CHD1	chr5:147161989-147162648	H1-hESC	embryonic stem cell:	n/a	n/a
8	GATA3	chr5:147161517-147162595	SK-N-SH	brain:	n/a	chr5:147161792-147161800 chr5:147162423-147162432
9	GATA2	chr5:147161587-147162630	SH-SY5Y	brain:	n/a	chr5:147162423-147162432
10	SIN3A	chr5:147161580-147162610	H1-hESC	embryonic stem cell:	n/a	chr5:147162383-147162396
11	CREB1	chr5:147161942-147162658	H1-hESC	embryonic stem cell:	n/a	n/a
12	JUND	chr5:147161835-147162648	H1-hESC	embryonic stem cell:	n/a	chr5:147162537-147162551
13	HDAC2	chr5:147162010-147162658	MCF-7	breast:	n/a	chr5:147162133-147162147
14	CTCF	chr5:147162420-147162570	HRPEpiC	eye:	n/a	n/a
15	CTCF	chr5:147162420-147162570	HCPEpiC	choroid plexus:	n/a	n/a
16	MXI1	chr5:147162249-147162585	H1-hESC	embryonic stem cell:	n/a	chr5:147162405-147162420 chr5:147162403-147162418
17	CTCF	chr5:147162386-147162587	Gliobla	brain:	n/a	chr5:147162392-147162405
18	MAX	chr5:147162227-147162624	H1-hESC	embryonic stem cell:	n/a	chr5:147162405-147162414
19	POLR2A	chr5:147161745-147162599	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr5:147161419-147162627	H1-neurons	neurons:	n/a	n/a
21	SP1	chr5:147162047-147162626	H1-hESC	embryonic stem cell:	n/a	chr5:147162347-147162356 chr5:147162444-147162453 chr5:147162360-147162369 chr5:147162328-147162339 chr5:147162360-147162370 chr5:147162440-147162454 chr5:147162345-147162356 chr5:147162443-147162455 chr5:147162359-147162370
22	RAD21	chr5:147161930-147162622	SK-N-SH_RA	brain:	n/a	chr5:147162193-147162200
23	EP300	chr5:147162013-147162611	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr5:147161926-147162604	H1-hESC	embryonic stem cell:	n/a	chr5:147162444-147162455
25	POLR2A	chr5:147161526-147162691	H1-neurons	neurons:	n/a	n/a
26	SP1	chr5:147161939-147162701	H1-hESC	embryonic stem cell:	n/a	chr5:147162347-147162356 chr5:147162444-147162453 chr5:147162360-147162369 chr5:147162328-147162339 chr5:147162360-147162370 chr5:147162440-147162454 chr5:147162345-147162356 chr5:147162443-147162455 chr5:147162359-147162370
27	GATA3	chr5:147161459-147162651	SK-N-SH	brain:	n/a	chr5:147161792-147161800 chr5:147162423-147162432
28	ZNF263	chr5:147161631-147162644	HEK293-T-REx	kidney:	n/a	chr5:147162261-147162270
29	REST	chr5:147161984-147162571	SK-N-SH	brain:	n/a	chr5:147162383-147162396 chr5:147162386-147162399
30	TAF1	chr5:147161522-147162693	H1-neurons	neurons:	n/a	n/a
31	MAX	chr5:147162049-147162612	SK-N-SH	brain:	n/a	chr5:147162405-147162414
32	RAD21	chr5:147162328-147162581	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr5:147161818-147162599	H1-hESC	embryonic stem cell:	n/a	chr5:147162193-147162200
34	POLR2A	chr5:147161781-147162623	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr5:147162277-147162572	H1-hESC	embryonic stem cell:	n/a	chr5:147162392-147162405
36	RAD21	chr5:147162091-147162670	H1-hESC	embryonic stem cell:	n/a	chr5:147162193-147162200
37	YY1	chr5:147161573-147162578	SK-N-SH_RA	brain:	n/a	chr5:147162444-147162455 chr5:147161804-147161820
38	EP300	chr5:147162028-147162568	SK-N-SH_RA	brain:	n/a	n/a
39	CTCF	chr5:147162460-147162610	HRPEpiC	eye:	n/a	n/a
40	ELF1	chr5:147161975-147162571	MCF-7	breast:	n/a	n/a
41	EP300	chr5:147162179-147162639	H1-hESC	embryonic stem cell:	n/a	n/a
42	YY1	chr5:147161829-147162642	H1-hESC	embryonic stem cell:	n/a	chr5:147162444-147162455
43	POLR2A	chr5:147161763-147162574	U87	brain:	n/a	n/a

Variant related genes	Relation type
JAKMIP2	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10477342	0.84[EUR][1000 genomes]
rs12659905	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17497858	0.84[EUR][1000 genomes]
rs17497914	0.82[EUR][1000 genomes]
rs17498180	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17563872	0.85[EUR][1000 genomes]
rs17624756	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17703007	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116770	0.84[EUR][1000 genomes]
rs28469761	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32204	0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4593256	0.84[EUR][1000 genomes]
rs4705042	0.84[EUR][1000 genomes]
rs6895952	0.81[EUR][1000 genomes]
rs7735973	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686888	0.92[AMR][1000 genomes];0.91[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	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6873548	SH3RF2	cis	parietal	SCAN
rs6873548	JAKMIP2	cis	Artery Tibial	GTEx
rs6873548	MRPL45	trans	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147159400-147162800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:147159600-147162800	Active TSS	Brain Hippocampus Middle	brain
3	chr5:147159800-147162600	Active TSS	Brain Germinal Matrix	brain
4	chr5:147159800-147162800	Active TSS	Fetal Brain Female	brain
5	chr5:147160000-147162600	Active TSS	Brain Angular Gyrus	brain
6	chr5:147160000-147162800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:147160200-147162600	Active TSS	Stomach Smooth Muscle	stomach
8	chr5:147160400-147162600	Active TSS	Brain Substantia Nigra	brain
9	chr5:147160400-147162800	Active TSS	Brain Anterior Caudate	brain
10	chr5:147160400-147162800	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr5:147160600-147162600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr5:147160600-147162600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr5:147160600-147162800	Active TSS	Brain Cingulate Gyrus	brain
14	chr5:147161200-147162600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:147162000-147162600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr5:147162000-147162600	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr5:147162000-147162600	Active TSS	Muscle Satellite Cultured Cells	--
18	chr5:147162200-147162600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr5:147162200-147162600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:147162200-147162600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
21	chr5:147162200-147162800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:147162200-147165400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:147162400-147162600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:147162400-147162600	Enhancers	Primary B cells from peripheral blood	blood
25	chr5:147162400-147162600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr5:147162400-147162600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr5:147162400-147162600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:147162400-147162600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:147162400-147162600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr5:147162400-147162600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:147162400-147162600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:147162400-147162600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr5:147162400-147162600	Enhancers	Thymus	Thymus
34	chr5:147162400-147162800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:147162400-147162800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr5:147162400-147162800	Weak transcription	Fetal Lung	lung
37	chr5:147162400-147163000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:147162400-147163000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:147162400-147163000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr5:147162400-147163000	Enhancers	Fetal Thymus	thymus
41	chr5:147162400-147163200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:147162400-147164000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:147162400-147167000	Weak transcription	Colon Smooth Muscle	Colon

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