Variant report

Variant	rs1684395
Chromosome Location	chr12:39083161-39083162
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	POLR2A	chr12:39083003-39083372	H1-neurons	neurons:	n/a	n/a
2	CTCF	chr12:39083140-39083290	HAc	cerebellar:	n/a	n/a
3	POLR2A	chr12:39083020-39083417	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
CPNE8	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10400455	0.83[JPT][hapmap]
rs10875959	0.88[YRI][hapmap]
rs10875962	0.88[YRI][hapmap]
rs10875963	0.88[YRI][hapmap]
rs10875979	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10875991	0.88[EUR][1000 genomes]
rs10876086	0.88[CEU][hapmap]
rs1095575	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168985	0.86[EUR][1000 genomes]
rs11169031	0.86[EUR][1000 genomes]
rs11169068	0.83[JPT][hapmap]
rs11169142	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169144	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169169	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11169301	0.86[EUR][1000 genomes]
rs11169387	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11169508	0.85[CEU][hapmap]
rs11169547	0.89[CEU][hapmap]
rs11612004	0.85[CEU][hapmap]
rs12322306	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12581365	0.83[JPT][hapmap]
rs1352122	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1352123	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1403523	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1486345	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1486346	0.83[JPT][hapmap]
rs1486357	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1554550	0.85[CEU][hapmap]
rs1601579	0.85[CEU][hapmap]
rs1684405	0.81[YRI][hapmap]
rs1684406	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1684407	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1684411	0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1684413	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1684414	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1684415	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1684416	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1719830	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1719848	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1719852	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1719853	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1719854	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1719855	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1719856	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1719858	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2069211	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs2101370	0.88[YRI][hapmap]
rs34254519	0.87[EUR][1000 genomes]
rs4768328	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768330	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55828987	0.86[EUR][1000 genomes]
rs6580726	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580755	0.88[CEU][hapmap]
rs7136593	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7301104	0.85[CEU][hapmap]
rs7957523	0.88[YRI][hapmap]
rs7973992	0.80[CEU][hapmap]
rs826838	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs826851	0.92[CEU][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826855	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs826856	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826858	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826870	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826873	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826874	0.84[EUR][1000 genomes]
rs826876	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs826878	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs826879	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs826881	0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs826886	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826888	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs826889	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs826891	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826892	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826893	0.89[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs844115	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs851934	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs860400	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs864324	0.83[MEX][hapmap];0.85[EUR][1000 genomes]
rs864325	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9645814	0.88[YRI][hapmap]
rs980571	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs980572	0.89[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs980573	0.91[EUR][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	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1045040	chr12:39038114-39084094	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1684395	ALG10B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39046000-39085400	Weak transcription	Aorta	Aorta
2	chr12:39055800-39100800	Weak transcription	NHEK	skin
3	chr12:39056000-39092200	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
6	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
7	chr12:39066600-39083400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:39074400-39098800	Weak transcription	Right Ventricle	heart
10	chr12:39079200-39114400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:39080600-39085400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:39080600-39085600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:39080600-39086600	Weak transcription	GM12878-XiMat	blood
14	chr12:39080600-39086800	Weak transcription	Ovary	ovary
15	chr12:39080600-39088600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:39080600-39089400	Weak transcription	A549	lung
17	chr12:39080600-39115600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:39080800-39083200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:39080800-39085400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:39080800-39086000	Strong transcription	Liver	Liver
21	chr12:39080800-39086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:39080800-39087400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:39080800-39092400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr12:39080800-39094200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:39080800-39094200	Weak transcription	Lung	lung
26	chr12:39080800-39095800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:39080800-39096200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:39080800-39097400	Weak transcription	Fetal Intestine Small	intestine
29	chr12:39080800-39098600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr12:39080800-39105000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:39081600-39085800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:39081600-39087600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr12:39082600-39085400	Weak transcription	Colonic Mucosa	Colon
34	chr12:39082800-39087800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:39083000-39083400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:39083000-39083400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:39083000-39083400	Strong transcription	Left Ventricle	heart
38	chr12:39083000-39083400	Enhancers	Osteobl	bone
39	chr12:39083000-39084200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:39083000-39085600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:39083000-39085600	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links