Variant report

Variant	rs13152799
Chromosome Location	chr4:147560411-147560412
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	POLR2A	chr4:147559917-147563587	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr4:147559935-147562474	H1-neurons	neurons:	n/a	n/a
3	SUZ12	chr4:147558103-147562402	NT2-D1	testis:	n/a	n/a
4	CTBP2	chr4:147559162-147562308	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr4:147560066-147560603	IMR90	lung:	n/a	n/a
6	SIN3A	chr4:147558992-147560802	H1-hESC	embryonic stem cell:	n/a	chr4:147559810-147559821 chr4:147560197-147560206
7	CTCF	chr4:147560280-147560430	WERI-Rb-1	eye:	n/a	n/a
8	CTCF	chr4:147560269-147560411	Fibrobl	skin:	n/a	n/a
9	MAX	chr4:147559887-147560608	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr4:147559691-147560630	H1-hESC	embryonic stem cell:	n/a	chr4:147560160-147560170 chr4:147559770-147559780
11	MAX	chr4:147560147-147560497	H1-hESC	embryonic stem cell:	n/a	n/a
12	SUZ12	chr4:147559999-147562291	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr4:147559882-147560614	H1-hESC	embryonic stem cell:	n/a	chr4:147560160-147560170
14	EGR1	chr4:147559693-147560488	H1-hESC	embryonic stem cell:	n/a	chr4:147559815-147559825 chr4:147559725-147559738 chr4:147560156-147560166 chr4:147559790-147559803 chr4:147560034-147560047
15	REST	chr4:147560005-147560612	HL-60	blood:	n/a	chr4:147560271-147560281
16	MAX	chr4:147560127-147560477	SK-N-SH	brain:	n/a	n/a
17	MAX	chr4:147559642-147560630	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000264323	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10011145	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10024327	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13134193	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1504360	0.85[CEU][hapmap]
rs1910595	0.89[ASN][1000 genomes]
rs34375288	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3762842	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827594	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6537430	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6856128	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv830107	chr4:147452434-147635720	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv880238	chr4:147469559-147617963	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv2753640	chr4:147538395-147641395	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv2754145	chr4:147538395-147641395	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv822768	chr4:147556986-147562654	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147558000-147562000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr4:147558000-147562000	Enhancers	Pancreas	Pancrea
3	chr4:147558200-147560600	Bivalent/Poised TSS	NH-A	brain
4	chr4:147558200-147561200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:147558200-147561800	Bivalent Enhancer	Lung	lung
6	chr4:147558200-147562200	Bivalent Enhancer	Fetal Brain Male	brain
7	chr4:147558400-147560600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:147558400-147561000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
9	chr4:147558800-147561000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:147558800-147561000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
11	chr4:147558800-147561800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr4:147559000-147560600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr4:147559000-147560600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:147559000-147560600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr4:147559000-147560600	Bivalent Enhancer	Esophagus	oesophagus
16	chr4:147559000-147560800	Bivalent Enhancer	Liver	Liver
17	chr4:147559000-147561000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr4:147559000-147562200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr4:147559200-147560600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr4:147559200-147560600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:147559200-147560600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:147559200-147560600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:147559200-147560800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:147559200-147560800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr4:147559200-147560800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
26	chr4:147559200-147561000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr4:147559600-147560600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:147559600-147560600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
29	chr4:147559600-147560800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
30	chr4:147559600-147560800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
31	chr4:147559600-147561600	Enhancers	Gastric	stomach
32	chr4:147559600-147562200	Bivalent Enhancer	Spleen	Spleen
33	chr4:147559800-147560600	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:147559800-147560600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:147559800-147560600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
36	chr4:147559800-147560600	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr4:147560000-147560600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:147560000-147560600	Bivalent/Poised TSS	HSMMtube	muscle
39	chr4:147560000-147560800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:147560000-147560800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:147560000-147560800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
42	chr4:147560000-147560800	Bivalent Enhancer	Fetal Muscle Leg	muscle
43	chr4:147560200-147560600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:147560200-147560600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
45	chr4:147560200-147560600	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
46	chr4:147560200-147560600	Flanking Active TSS	Right Atrium	heart
47	chr4:147560200-147560600	Flanking Bivalent TSS/Enh	Right Ventricle	heart
48	chr4:147560200-147560800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr4:147560200-147560800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:147560200-147561000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links