Variant report

Variant	rs16826512
Chromosome Location	chr2:134326481-134326482
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	TCF12	chr2:134325763-134326482	A549	lung:	n/a	chr2:134326452-134326459

Variant related genes	Relation type
NCKAP5	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10803537	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11675147	0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs12622133	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13412991	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs16826437	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16826737	1.00[EUR][1000 genomes]
rs1897433	0.91[CHB][hapmap]
rs60546774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6705688	1.00[ASW][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6706405	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs876204	1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs978097	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
3	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv516644	chr2:134301130-134391214	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16826512	RHOXF2	trans	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134324400-134327000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:134324400-134327200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:134324400-134329000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:134324600-134328600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr2:134324600-134329600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr2:134324600-134330400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:134324800-134326600	Active TSS	Brain Anterior Caudate	brain
8	chr2:134325000-134330000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:134325000-134342400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:134325200-134329000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:134325400-134331800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:134325600-134327000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr2:134326000-134326600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:134326000-134327200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr2:134326000-134327600	Enhancers	Fetal Heart	heart
16	chr2:134326000-134328200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:134326200-134326600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:134326200-134326600	Enhancers	HUVEC	blood vessel
19	chr2:134326200-134326800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr2:134326200-134326800	Weak transcription	Left Ventricle	heart
21	chr2:134326200-134327000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr2:134326200-134327000	Enhancers	Fetal Muscle Leg	muscle
23	chr2:134326200-134327000	Enhancers	Stomach Mucosa	stomach
24	chr2:134326200-134327200	Enhancers	Fetal Intestine Small	intestine
25	chr2:134326200-134329600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:134326200-134329800	Weak transcription	Esophagus	oesophagus
27	chr2:134326200-134337000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:134326400-134326600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:134326400-134326600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:134326400-134326600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:134326400-134326600	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:134326400-134326600	Enhancers	Brain Hippocampus Middle	brain
33	chr2:134326400-134326600	Weak transcription	Brain Substantia Nigra	brain
34	chr2:134326400-134326600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
35	chr2:134326400-134326600	Weak transcription	Fetal Brain Female	brain
36	chr2:134326400-134326600	Enhancers	Fetal Intestine Large	intestine
37	chr2:134326400-134326600	Enhancers	NHEK	skin
38	chr2:134326400-134326800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:134326400-134326800	Enhancers	A549	lung
40	chr2:134326400-134327000	Enhancers	Brain Angular Gyrus	brain
41	chr2:134326400-134327200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:134326400-134327200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:134326400-134327200	Enhancers	Fetal Stomach	stomach
44	chr2:134326400-134327200	Enhancers	NHDF-Ad	bronchial
45	chr2:134326400-134327200	Enhancers	NHLF	lung
46	chr2:134326400-134327400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:134326400-134327400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr2:134326400-134327400	Enhancers	Fetal Lung	lung
49	chr2:134326400-134327400	Enhancers	NH-A	brain
50	chr2:134326400-134328200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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