Variant report

Variant	rs11168698
Chromosome Location	chr12:49107298-49107299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49082621..49084947-chr12:49105438..49107834,2	K562	blood:
2	chr12:49105788..49107564-chr12:49110474..49111999,2	K562	blood:
3	chr12:49103301..49108658-chr12:49108679..49112078,7	K562	blood:
4	chr12:49106870..49108564-chr12:49207751..49210118,2	MCF-7	breast:
5	chr12:49072707..49077771-chr12:49103757..49111723,15	MCF-7	breast:
6	chr12:49075363..49077740-chr12:49105945..49108100,2	K562	blood:

Variant related genes	Relation type
ENSG00000139620	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000167535	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10747554	0.92[ASN][1000 genomes]
rs10783273	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783274	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10783275	0.84[ASN][1000 genomes]
rs10783278	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875849	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10875850	0.85[ASN][1000 genomes]
rs10875852	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875853	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875861	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10875862	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875863	0.89[EUR][1000 genomes]
rs1110432	0.97[ASN][1000 genomes]
rs11168657	0.83[ASN][1000 genomes]
rs11168665	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168674	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168681	0.81[CEU][hapmap];0.93[TSI][hapmap]
rs11168697	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168702	0.81[JPT][hapmap]
rs12299955	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12426435	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1316514	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1895995	0.89[ASN][1000 genomes]
rs2114320	0.93[ASN][1000 genomes]
rs2162317	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277365	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2277366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2291728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409085	0.88[ASN][1000 genomes]
rs2898087	0.89[ASN][1000 genomes]
rs3209584	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs35717253	0.89[ASN][1000 genomes]
rs3741628	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3741629	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3741630	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3741632	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3803025	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3943899	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4113946	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4500528	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760735	0.85[ASN][1000 genomes]
rs4760737	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760739	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760740	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6580689	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6580690	0.89[ASN][1000 genomes]
rs7133756	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7136021	0.85[EUR][1000 genomes]
rs7138190	0.89[ASN][1000 genomes]
rs7139236	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]
rs7299276	0.91[ASN][1000 genomes]
rs7304711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs7305907	0.97[ASN][1000 genomes]
rs7306604	0.97[ASN][1000 genomes]
rs7308699	0.95[ASN][1000 genomes]
rs7314665	0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7954446	0.95[ASN][1000 genomes]
rs7954548	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs7964546	0.96[ASN][1000 genomes]
rs7966065	0.84[ASN][1000 genomes]
rs7973824	0.82[ASN][1000 genomes]
rs7974625	0.96[ASN][1000 genomes]
rs7975030	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7975821	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332441	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9634241	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9634242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9634262	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11168698	C12orf41	cis	parietal	SCAN
rs11168698	KANSL2	cis	Nerve Tibial	GTEx
rs11168698	FAM186B	cis	cerebellum	SCAN
rs11168698	KANSL2	cis	Thyroid	GTEx
rs11168698	KANSL2	cis	Artery Tibial	GTEx
rs11168698	KANSL2	cis	lung	GTEx
rs11168698	C12orf41	cis	cerebellum	SCAN
rs11168698	KANSL2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49076600-49109000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:49081600-49107600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:49081600-49108400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:49082000-49107600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr12:49082200-49107400	Strong transcription	Placenta	Placenta
6	chr12:49082200-49108000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:49082200-49108400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr12:49082200-49108600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:49082200-49108600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:49082200-49108800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:49082600-49107600	Strong transcription	Fetal Thymus	thymus
12	chr12:49088200-49107400	Weak transcription	Psoas Muscle	Psoas
13	chr12:49088200-49107600	Weak transcription	Stomach Mucosa	stomach
14	chr12:49089800-49109400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:49090000-49107600	Weak transcription	Brain Angular Gyrus	brain
16	chr12:49090000-49107800	Weak transcription	Fetal Heart	heart
17	chr12:49090000-49108400	Weak transcription	Fetal Brain Male	brain
18	chr12:49091800-49107400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:49093400-49108000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr12:49095000-49108600	Strong transcription	Fetal Stomach	stomach
21	chr12:49095600-49107400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:49095600-49107800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:49095600-49108800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:49095800-49107600	Strong transcription	A549	lung
25	chr12:49095800-49108400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:49096000-49107400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr12:49097600-49108600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:49097600-49109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:49097800-49108400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:49098200-49107600	Weak transcription	Colon Smooth Muscle	Colon
31	chr12:49098200-49107800	Weak transcription	Fetal Kidney	kidney
32	chr12:49098200-49109600	Weak transcription	Aorta	Aorta
33	chr12:49098400-49107400	Weak transcription	Pancreas	Pancrea
34	chr12:49098600-49107400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr12:49098800-49108600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:49099200-49108600	Weak transcription	Gastric	stomach
37	chr12:49099200-49108800	Weak transcription	Brain Substantia Nigra	brain
38	chr12:49099400-49107400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:49099400-49108400	Weak transcription	Right Ventricle	heart
40	chr12:49099600-49108000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:49099600-49108000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:49099600-49108200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:49099600-49109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:49099800-49107400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr12:49099800-49107400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:49099800-49108600	Weak transcription	Esophagus	oesophagus
47	chr12:49100200-49107400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr12:49100800-49107800	Strong transcription	Fetal Muscle Leg	muscle
49	chr12:49100800-49108200	Strong transcription	Fetal Intestine Small	intestine
50	chr12:49101000-49109000	Weak transcription	HSMMtube	muscle

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