Variant report

Variant	rs13796
Chromosome Location	chr1:154245917-154245918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154245648-154245974	HL-60	blood:	n/a	n/a
2	POLR2A	chr1:154245684-154246404	K562	blood:	n/a	n/a
3	JUN	chr1:154244466-154246507	K562	blood:	n/a	n/a
4	MXI1	chr1:154244035-154246094	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr1:154245852-154246483	PFSK-1	brain:	n/a	n/a
6	ZNF263	chr1:154244673-154245949	HEK293-T-REx	kidney:	n/a	chr1:154244908-154244929

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154244115..154246363-chr1:154579238..154580739,2	MCF-7	breast:
2	chr1:154154597..154158912-chr1:154243474..154246502,4	K562	blood:
3	chr1:154226522..154228397-chr1:154244257..154246291,2	MCF-7	breast:
4	chr1:154244396..154246200-chr1:154300299..154302808,2	MCF-7	breast:
5	chr1:153962369..153964805-chr1:154243433..154246826,4	MCF-7	breast:
6	chr1:154191724..154193429-chr1:154244687..154246204,2	MCF-7	breast:
7	chr1:154191842..154194909-chr1:154241050..154247826,7	K562	blood:
8	chr1:154162391..154165167-chr1:154243401..154246301,3	K562	blood:
9	chr1:154245017..154247132-chr20:55840387..55841981,2	MCF-7	breast:
10	chr1:154243817..154246754-chr1:154291993..154294660,2	K562	blood:
11	chr1:154244884..154247394-chr1:154296390..154298976,2	K562	blood:
12	chr1:153963157..153965644-chr1:154243334..154246314,2	K562	blood:
13	chr1:154153295..154155841-chr1:154244913..154246544,2	MCF-7	breast:
14	chr1:154236442..154241812-chr1:154243586..154247600,7	MCF-7	breast:

No data

Variant related genes	Relation type
HAX1	TF binding region
ENSG00000252817	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000143595	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000160710	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10797061	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10908751	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11584755	0.90[ASN][1000 genomes]
rs11586916	0.90[ASN][1000 genomes]
rs1194580	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1194582	0.85[ASN][1000 genomes]
rs1194599	0.85[ASN][1000 genomes]
rs1194600	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1194602	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1194603	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1194604	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12044616	0.85[ASN][1000 genomes]
rs12142550	0.90[ASN][1000 genomes]
rs12354278	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220390	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4072431	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4364874	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4393149	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4845609	0.85[ASN][1000 genomes]
rs4845610	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs61807361	1.00[ASN][1000 genomes]
rs6667222	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7521837	0.90[ASN][1000 genomes]
rs7526644	0.85[ASN][1000 genomes]
rs9803862	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9804045	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9943097	0.85[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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13796	SPRR4	cis	cerebellum	SCAN
rs13796	GBA	cis	parietal	SCAN
rs13796	FAM63A	cis	cerebellum	SCAN
rs13796	TDRD10	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154244000-154246000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:154244200-154246000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:154244200-154246200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:154244200-154246200	Active TSS	A549	lung
5	chr1:154244200-154246400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:154244400-154246000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:154244400-154246000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:154244400-154246000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:154244400-154246000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:154244400-154246000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:154244400-154246000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:154244400-154246000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:154244400-154246000	Active TSS	Fetal Kidney	kidney
14	chr1:154244400-154246000	Active TSS	Right Atrium	heart
15	chr1:154244400-154246000	Active TSS	NHDF-Ad	bronchial
16	chr1:154244400-154246200	Active TSS	HSMMtube	muscle
17	chr1:154244400-154246400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr1:154244600-154246000	Active TSS	HSMM	muscle
19	chr1:154244600-154246200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:154245000-154246000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:154245000-154246000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:154245200-154246000	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr1:154245200-154246000	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr1:154245200-154246000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr1:154245200-154246000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr1:154245200-154246000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:154245200-154246200	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr1:154245200-154246200	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr1:154245400-154246000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr1:154245400-154246000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:154245400-154246000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr1:154245400-154246000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr1:154245400-154246000	Flanking Active TSS	Liver	Liver
34	chr1:154245400-154246000	Flanking Active TSS	Fetal Muscle Trunk	muscle
35	chr1:154245400-154246000	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr1:154245400-154246000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr1:154245400-154246200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:154245400-154246200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr1:154245400-154246200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr1:154245400-154246200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:154245400-154246200	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr1:154245400-154246200	Flanking Active TSS	Colonic Mucosa	Colon
43	chr1:154245400-154246200	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr1:154245400-154246200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr1:154245400-154246200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr1:154245400-154246200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr1:154245400-154246200	Flanking Active TSS	Osteobl	bone
48	chr1:154245400-154246400	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr1:154245600-154246000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:154245600-154246000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links