Variant report

Variant	rs12993598
Chromosome Location	chr2:10080880-10080881
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	chr2:10080832-10081290	HepG2	liver:	n/a	n/a
2	ZBTB7A	chr2:10080771-10080915	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10080626..10083275-chr2:10089838..10091585,2	K562	blood:
2	chr2:10079779..10081937-chr2:10082992..10085179,2	MCF-7	breast:
3	chr2:10075342..10078182-chr2:10080340..10082783,2	K562	blood:

Variant related genes	Relation type
GRHL1	TF binding region
ENSG00000269973	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1044645	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12464130	0.97[ASN][1000 genomes]
rs12473353	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12993610	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13071	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2288643	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3748999	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4669504	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12993598	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs12993598	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:10059400-10081200	Weak transcription	GM12878-XiMat	blood
6	chr2:10073400-10081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:10073400-10084400	Weak transcription	Lung	lung
8	chr2:10073600-10088800	Weak transcription	Spleen	Spleen
9	chr2:10073800-10081000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:10073800-10082000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:10074000-10081800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:10074200-10081800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:10075600-10082400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:10075800-10081200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:10075800-10081600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:10075800-10081600	Weak transcription	Placenta	Placenta
17	chr2:10076000-10081400	Weak transcription	Fetal Thymus	thymus
18	chr2:10076000-10081600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:10078200-10081400	Weak transcription	A549	lung
20	chr2:10079200-10082400	Enhancers	Fetal Lung	lung
21	chr2:10079600-10081000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:10079600-10081000	Enhancers	Fetal Intestine Large	intestine
23	chr2:10079600-10081200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:10079600-10082200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:10079800-10081000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr2:10079800-10081600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:10079800-10082000	Enhancers	Stomach Mucosa	stomach
28	chr2:10079800-10082600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:10079800-10082600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:10080000-10081200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:10080000-10081200	Enhancers	Osteobl	bone
32	chr2:10080000-10081800	Weak transcription	K562	blood
33	chr2:10080000-10082200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr2:10080200-10081000	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr2:10080200-10081200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:10080200-10082600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr2:10080400-10081600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:10080400-10081800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:10080600-10081000	Enhancers	Colonic Mucosa	Colon
40	chr2:10080600-10081000	Flanking Active TSS	HepG2	liver
41	chr2:10080600-10081000	Enhancers	HSMMtube	muscle
42	chr2:10080600-10081200	Enhancers	Esophagus	oesophagus
43	chr2:10080600-10081600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:10080600-10081800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:10080600-10082400	Enhancers	Gastric	stomach
46	chr2:10080600-10082600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr2:10080800-10081000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:10080800-10081000	Flanking Active TSS	HSMM	muscle
49	chr2:10080800-10081200	Enhancers	Fetal Intestine Small	intestine
50	chr2:10080800-10081200	Enhancers	Pancreas	Pancrea

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