Variant report

Variant	rs1054611
Chromosome Location	chr12:10170161-10170162
allele	G/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	JUN	chr12:10169471-10170437	HUVEC	blood vessel:	n/a	n/a
2	GATA2	chr12:10169473-10170761	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:10169416-10170178	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
CLEC1B	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10400568	0.83[JPT][hapmap]
rs1075996	0.85[JPT][hapmap]
rs1807355	0.84[JPT][hapmap]
rs1868212	0.84[JPT][hapmap]
rs4764188	0.85[JPT][hapmap]
rs494312	0.92[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs620449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7305054	0.85[JPT][hapmap];0.80[MEX][hapmap]
rs7305223	0.85[JPT][hapmap]
rs7960202	0.85[JPT][hapmap]
rs7970682	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043125	chr12:10121288-10177037	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1042106	chr12:10121288-10177636	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1040610	chr12:10121288-10179374	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv898756	chr12:10142538-10174314	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Sensory disturbances after bilateral sagittal split ramus osteotomy	23834954	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1054611	ATN1	cis	cerebellum	SCAN
rs1054611	CLEC12B	cis	Whole Blood	GTEx
rs1054611	TAS2R43	cis	cerebellum	SCAN
rs1054611	NCAPD2	cis	cerebellum	SCAN
rs1054611	LEPREL2	cis	parietal	SCAN
rs1054611	CLEC12A	cis	Whole Blood	GTEx
rs1054611	RP11-133L14.5	cis	Whole Blood	GTEx
rs1054611	SCARNA12	cis	cerebellum	SCAN
rs1054611	CLEC12A	cis	Artery Tibial	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10163200-10170200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:10167600-10170800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:10168800-10171600	Enhancers	HUVEC	blood vessel
4	chr12:10169200-10170600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr12:10169400-10170200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:10169400-10170200	Enhancers	A549	lung
7	chr12:10169400-10170400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr12:10169400-10170400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr12:10169400-10170400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr12:10169400-10170400	Enhancers	HMEC	breast
11	chr12:10169400-10170600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr12:10169400-10170600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr12:10169400-10170600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
14	chr12:10169600-10170200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:10169600-10170200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr12:10169600-10170200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:10169600-10170400	Enhancers	Hela-S3	cervix
18	chr12:10169600-10171600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr12:10169600-10171800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:10169800-10170200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:10169800-10170200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:10169800-10170400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr12:10169800-10170400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:10169800-10172200	Enhancers	Primary hematopoietic stem cells	blood
25	chr12:10170000-10170200	Enhancers	Esophagus	oesophagus
26	chr12:10170000-10171000	Enhancers	Stomach Smooth Muscle	stomach
27	chr12:10170000-10171600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:10170000-10172000	Enhancers	Fetal Stomach	stomach

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