Variant report

Variant	rs10483885
Chromosome Location	chr14:78171842-78171843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78170877..78172859-chr14:78173007..78174927,2	K562	blood:
2	chr14:78166641..78172350-chr14:78172652..78176323,11	MCF-7	breast:
3	chr14:78169975..78173523-chr14:78173651..78176580,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100601	Chromatin interaction
ENSG00000119705	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1006038	0.90[CHB][hapmap]
rs1006039	0.90[CHB][hapmap]
rs1006040	0.90[CHB][hapmap]
rs1008988	0.95[CHB][hapmap]
rs10134425	0.97[ASN][1000 genomes]
rs10138747	0.89[ASN][1000 genomes]
rs10139492	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10142722	0.90[CHB][hapmap]
rs10143249	0.89[ASN][1000 genomes]
rs10143294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10144448	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10146255	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1048147	0.90[CHB][hapmap]
rs114763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11621719	0.85[ASN][1000 genomes]
rs11622761	0.85[ASN][1000 genomes]
rs11624118	0.85[ASN][1000 genomes]
rs11628888	0.85[CHB][hapmap]
rs11846215	0.82[ASN][1000 genomes]
rs12587155	0.81[CEU][hapmap]
rs12879880	0.89[ASN][1000 genomes]
rs12880300	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12885306	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap]
rs12886631	0.88[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs12887313	0.89[ASN][1000 genomes]
rs12890728	0.85[CHB][hapmap]
rs12890828	0.84[ASN][1000 genomes]
rs1477262	0.90[CHB][hapmap]
rs1477263	0.90[ASN][1000 genomes]
rs1477264	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17106157	0.90[CHB][hapmap]
rs176941	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs176943	0.90[CHB][hapmap]
rs176946	0.90[CHB][hapmap]
rs176947	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176948	0.98[ASN][1000 genomes]
rs176951	0.90[CHB][hapmap]
rs176954	0.98[ASN][1000 genomes]
rs176955	0.90[CHB][hapmap]
rs176956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs176959	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs176961	0.97[ASN][1000 genomes]
rs176963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs176964	0.90[CHB][hapmap];0.97[ASN][1000 genomes]
rs176965	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs176968	0.97[ASN][1000 genomes]
rs176969	0.97[ASN][1000 genomes]
rs176970	0.97[ASN][1000 genomes]
rs176972	0.96[ASN][1000 genomes]
rs176975	0.97[ASN][1000 genomes]
rs176976	0.97[ASN][1000 genomes]
rs176977	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176980	0.90[CHB][hapmap]
rs2080703	0.92[ASN][1000 genomes]
rs2111831	0.81[ASN][1000 genomes]
rs2267755	0.81[CEU][hapmap]
rs2267756	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs2267759	0.90[CHB][hapmap]
rs2267760	0.90[CHB][hapmap]
rs2267761	0.90[CHB][hapmap]
rs2267762	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2267763	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2267764	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2277917	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2284233	0.98[ASN][1000 genomes]
rs2284234	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2284235	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2299930	0.90[CHB][hapmap]
rs2299931	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs3759728	0.90[CHB][hapmap]
rs3783980	0.90[CHB][hapmap]
rs3783981	0.92[ASN][1000 genomes]
rs3783982	0.92[ASN][1000 genomes]
rs4632066	0.90[CHB][hapmap]
rs4641655	0.89[ASN][1000 genomes]
rs4899670	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs4899673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899674	0.95[ASN][1000 genomes]
rs4903624	0.84[CEU][hapmap]
rs4903626	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4903638	0.90[ASN][1000 genomes]
rs61992864	0.80[ASN][1000 genomes]
rs61992867	0.83[ASN][1000 genomes]
rs61992868	0.83[ASN][1000 genomes]
rs6574392	0.93[ASN][1000 genomes]
rs6574394	0.93[ASN][1000 genomes]
rs6574399	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6574404	0.86[CHB][hapmap]
rs7142390	0.90[CHB][hapmap]
rs7143926	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7145717	0.90[ASN][1000 genomes]
rs7145979	0.86[CEU][hapmap]
rs7148078	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7148126	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7150531	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7151685	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7154571	0.87[ASN][1000 genomes]
rs7160355	0.92[ASN][1000 genomes]
rs717682	0.87[ASN][1000 genomes]
rs72210300	0.82[ASN][1000 genomes]
rs759713	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs8003691	0.90[CHB][hapmap]
rs8010541	0.93[ASN][1000 genomes]
rs8011337	0.90[CHB][hapmap]
rs8015645	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8016447	0.90[CHB][hapmap]
rs8022516	0.95[ASN][1000 genomes]
rs9323649	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9323650	0.90[CHB][hapmap]
rs9323651	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[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	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv520021	chr14:78152921-78208294	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10483885	ALDH6A1	cis	parietal	SCAN
rs10483885	RPS6KL1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78140400-78172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr14:78140600-78173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:78150400-78172200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr14:78152600-78172200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:78153400-78172000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr14:78154400-78172600	Weak transcription	Small Intestine	intestine
8	chr14:78156200-78172000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:78156800-78172400	Strong transcription	Dnd41	blood
10	chr14:78158600-78172800	Weak transcription	NHDF-Ad	bronchial
11	chr14:78163800-78172600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr14:78163800-78172600	Weak transcription	HMEC	breast
13	chr14:78163800-78173400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr14:78163800-78173400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr14:78163800-78173400	Weak transcription	Right Ventricle	heart
16	chr14:78164000-78173000	Weak transcription	HSMMtube	muscle
17	chr14:78164000-78173400	Weak transcription	Aorta	Aorta
18	chr14:78165800-78172600	Weak transcription	Fetal Heart	heart
19	chr14:78166400-78172200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr14:78166400-78172800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr14:78167000-78172000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:78167000-78172200	Strong transcription	Fetal Brain Female	brain
23	chr14:78167000-78172200	Strong transcription	Fetal Stomach	stomach
24	chr14:78167200-78172200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:78167400-78172000	Strong transcription	Brain Anterior Caudate	brain
26	chr14:78168000-78172000	Strong transcription	Osteobl	bone
27	chr14:78168000-78172800	Weak transcription	Psoas Muscle	Psoas
28	chr14:78169000-78173000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr14:78169200-78172800	Weak transcription	HUVEC	blood vessel
30	chr14:78169600-78173400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:78169800-78172800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr14:78169800-78172800	Weak transcription	Brain Germinal Matrix	brain
33	chr14:78170600-78172000	Strong transcription	Primary hematopoietic stem cells	blood
34	chr14:78170600-78173200	Weak transcription	Colonic Mucosa	Colon
35	chr14:78170800-78172600	Weak transcription	Colon Smooth Muscle	Colon
36	chr14:78170800-78172800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr14:78170800-78173200	Weak transcription	Gastric	stomach
38	chr14:78170800-78173400	Weak transcription	Pancreas	Pancrea
39	chr14:78171000-78172600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:78171000-78172600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr14:78171000-78172600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr14:78171000-78172600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr14:78171000-78172600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr14:78171000-78172600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr14:78171000-78172800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr14:78171000-78172800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr14:78171000-78172800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr14:78171000-78172800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr14:78171000-78172800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr14:78171000-78172800	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links