Variant report

Variant	rs1038497
Chromosome Location	chr12:104444423-104444424
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr12:104442977-104444428	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:104444418-104444468	MCF-7	breast:	n/a
2	chr12:104444418-104444468	HEEpiC	esophagus:	n/a
3	chr12:104444418-104444468	SKMC	muscle:	n/a
4	chr12:104444418-104444468	HUVEC	blood vessel:	n/a
5	chr12:104444418-104444468	A549	lung:	n/a
6	chr12:104444418-104444468	HCPEpiC	choroid plexus:	n/a
7	chr12:104444418-104444468	Jurkat	blood:	n/a
8	chr12:104444418-104444468	GM12878	blood:	n/a
9	chr12:104444418-104444468	HCM	heart:	n/a
10	chr12:104444418-104444468	GM12892	blood:	n/a
11	chr12:104444418-104444468	HepG2	liver:	n/a
12	chr12:104444418-104444468	CMK	blood:	n/a
13	chr12:104444418-104444468	AoSMC	blood vessel:	n/a
14	chr12:104444418-104444468	PANC-1	pancreas:	n/a
15	chr12:104444418-104444468	HL-60	blood:	n/a
16	chr12:104444418-104444468	BJ	skin:	n/a
17	chr12:104444418-104444468	SAEC	small airway:	n/a
18	chr12:104444418-104444468	BE2_C	brain:	n/a
19	chr12:104444418-104444468	HRCEpiC	kidney:	n/a
20	chr12:104444418-104444468	HCF	heart:	n/a
21	chr12:104444418-104444468	RPTEC	kidney:	n/a
22	chr12:104444418-104444468	LNCaP	prostate:	n/a
23	chr12:104444418-104444468	Hepatocyte	liver:	n/a
24	chr12:104444418-104444468	GM06990	blood:	n/a
25	chr12:104444418-104444468	AG10803	skin:	n/a
26	chr12:104444418-104444468	HIPEpiC	eye:	n/a
27	chr12:104444418-104444468	ProgFib	skin:	n/a
28	chr12:104444418-104444468	HEK293	kidney:	embryo
29	chr12:104444418-104444468	NB4	blood:	n/a
30	chr12:104444418-104444468	NT2-D1	testis:	n/a
31	chr12:104444418-104444468	AG04449	skin:	fetal
32	chr12:104444418-104444468	SK-N-SH	brain:	n/a
33	chr12:104444418-104444468	ovcar-3	ovarian:	n/a
34	chr12:104444418-104444468	K562	blood:	n/a
35	chr12:104444418-104444468	U87	brain:	n/a
36	chr12:104444418-104444468	Hela-S3	cervix:	n/a
37	chr12:104444418-104444468	HMEC	breast:	n/a
38	chr12:104444418-104444468	Caco-2	colon:	n/a
39	chr12:104444418-104444468	PFSK-1	brain:	n/a
40	chr12:104444418-104444468	NHDF-neo	bronchial:	n/a
41	chr12:104444418-104444468	AG09319	gingival:	n/a
42	chr12:104444418-104444468	AG04450	lung:	fetal
43	chr12:104444418-104444468	SK-N-SH_RA	brain:	n/a
44	chr12:104444418-104444468	GM19239	blood:	n/a
45	chr12:104444418-104444468	IMR90	lung:	fetal
46	chr12:104444418-104444468	T-47D	breast:	n/a
47	chr12:104444418-104444468	H1-hESC	embryonic stem cell:	embryo
48	chr12:104444418-104444468	ECC-1	luminal epithelium:	n/a
49	chr12:104444418-104444468	NH-A	brain:	n/a
50	chr12:104444418-104444468	SK-N-MC	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104359553..104362361-chr12:104443780..104446717,2	K562	blood:

No data

Variant related genes	Relation type
GLT8D2	TF binding region
GLT8D2	CpG island
ENSG00000139372	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11111876	0.90[ASN][1000 genomes]
rs12820602	0.83[JPT][hapmap]
rs2583228	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3751206	0.83[JPT][hapmap]
rs4135036	0.83[JPT][hapmap]
rs4135128	0.83[JPT][hapmap]
rs4135137	0.83[JPT][hapmap]
rs4964462	0.88[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104441800-104444600	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr12:104442400-104444600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:104442600-104444600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr12:104442600-104444600	Active TSS	Right Atrium	heart
5	chr12:104442800-104444600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr12:104442800-104444600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:104443000-104444600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:104443000-104444600	Active TSS	NHDF-Ad	bronchial
9	chr12:104443200-104444600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
10	chr12:104443400-104444600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:104443600-104444600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:104443600-104444600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:104443800-104444600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:104443800-104444600	Bivalent Enhancer	K562	blood
15	chr12:104444000-104444600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:104444000-104444600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:104444000-104444600	Flanking Active TSS	Osteobl	bone
18	chr12:104444000-104449000	Weak transcription	Pancreas	Pancrea
19	chr12:104444200-104444600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:104444200-104444600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
21	chr12:104444200-104444600	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr12:104444200-104444600	Flanking Active TSS	Fetal Lung	lung
23	chr12:104444200-104444600	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr12:104444200-104444600	Flanking Active TSS	HSMM	muscle
25	chr12:104444200-104444800	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr12:104444200-104449400	Weak transcription	Liver	Liver
27	chr12:104444400-104444600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr12:104444400-104444600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr12:104444400-104444600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:104444400-104444600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr12:104444400-104444600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:104444400-104444600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:104444400-104444600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:104444400-104444600	Enhancers	Brain Anterior Caudate	brain
35	chr12:104444400-104444600	Enhancers	Brain Hippocampus Middle	brain
36	chr12:104444400-104444600	Flanking Active TSS	Ovary	ovary
37	chr12:104444400-104444600	Bivalent Enhancer	HepG2	liver
38	chr12:104444400-104444600	Enhancers	HMEC	breast
39	chr12:104444400-104444600	Enhancers	HSMMtube	muscle
40	chr12:104444400-104444600	Active TSS	NHLF	lung
41	chr12:104444400-104444800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr12:104444400-104444800	Enhancers	Placenta	Placenta
43	chr12:104444400-104444800	Enhancers	Fetal Stomach	stomach
44	chr12:104444400-104448400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:104444400-104448600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:104444400-104449200	Weak transcription	Fetal Heart	heart
47	chr12:104444400-104457400	Weak transcription	Brain Cingulate Gyrus	brain

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