Variant report

Variant	rs12784975
Chromosome Location	chr10:98380137-98380138
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	chr10:98379904-98380950	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:98378430-98380231	PBDE	blood:	n/a	n/a
3	POLR2A	chr10:98379744-98380474	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PIK3AP1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1051450	0.84[MEX][hapmap]
rs10882827	0.83[AMR][1000 genomes]
rs11188847	0.89[MEX][hapmap]
rs11188858	0.84[AMR][1000 genomes]
rs11592791	0.82[ASN][1000 genomes]
rs12219275	0.87[LWK][hapmap];0.81[MKK][hapmap]
rs36098523	0.83[AMR][1000 genomes]
rs3748236	0.80[AMR][1000 genomes]
rs41317270	0.87[AMR][1000 genomes]
rs58305369	0.83[AMR][1000 genomes]
rs7073017	0.84[AMR][1000 genomes]
rs7073682	0.85[AMR][1000 genomes]
rs7074516	0.84[MEX][hapmap]
rs7091606	0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs8578	0.83[MEX][hapmap]

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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv895909	chr10:98354924-98382165	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12784975	CWF19L1	cis	cerebellum	SCAN
rs12784975	FRA10AC1	cis	parietal	SCAN
rs12784975	SCD	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98350800-98395600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr10:98352400-98399400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr10:98352600-98403000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr10:98353000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:98353000-98403000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr10:98354600-98388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:98357800-98382000	Strong transcription	GM12878-XiMat	blood
8	chr10:98360400-98392800	Weak transcription	Thymus	Thymus
9	chr10:98362200-98389200	Strong transcription	Primary B cells from cord blood	blood
10	chr10:98363800-98392600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:98366000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:98366600-98392600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:98367400-98418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr10:98371000-98382600	Strong transcription	Spleen	Spleen
15	chr10:98371000-98388600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr10:98371000-98389000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:98372200-98388600	Strong transcription	Primary hematopoietic stem cells	blood
18	chr10:98374400-98390200	Weak transcription	Small Intestine	intestine
19	chr10:98375600-98380800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr10:98375800-98390200	Weak transcription	Adipose Nuclei	Adipose
21	chr10:98376400-98380400	Enhancers	Fetal Heart	heart
22	chr10:98376400-98381200	Enhancers	Ovary	ovary
23	chr10:98376600-98380400	Enhancers	Left Ventricle	heart
24	chr10:98376800-98381000	Enhancers	Right Atrium	heart
25	chr10:98377000-98380800	Enhancers	Fetal Lung	lung
26	chr10:98377200-98384400	Enhancers	Stomach Mucosa	stomach
27	chr10:98377400-98392600	Weak transcription	Esophagus	oesophagus
28	chr10:98377600-98380400	Enhancers	Colon Smooth Muscle	Colon
29	chr10:98378200-98392600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr10:98378400-98380200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:98378400-98380200	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr10:98378400-98380200	Enhancers	HSMM	muscle
33	chr10:98378400-98380400	Enhancers	Duodenum Mucosa	Duodenum
34	chr10:98378400-98381200	Enhancers	Right Ventricle	heart
35	chr10:98378600-98380200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr10:98378600-98381000	Enhancers	Colonic Mucosa	Colon
37	chr10:98378600-98382000	Enhancers	Gastric	stomach
38	chr10:98378800-98381400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr10:98378800-98389400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr10:98378800-98392400	Weak transcription	Fetal Intestine Large	intestine
41	chr10:98378800-98392600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr10:98379000-98381800	Weak transcription	Brain Substantia Nigra	brain
43	chr10:98379000-98396200	Weak transcription	HepG2	liver
44	chr10:98379200-98387600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:98379400-98380200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr10:98379400-98382000	Enhancers	K562	blood
47	chr10:98379600-98392600	Strong transcription	Liver	Liver
48	chr10:98379800-98380200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:98379800-98380200	Genic enhancers	Lung	lung
50	chr10:98379800-98380400	Genic enhancers	Rectal Mucosa Donor 31	rectum

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