Variant report

Variant	rs1012154
Chromosome Location	chr12:31627584-31627585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10743757	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10743758	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs10771832	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs10843947	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs11051418	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs11051437	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs11051441	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1150942	0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1150943	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1150945	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1150950	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1150953	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1150954	0.81[CEU][hapmap];0.92[CHB][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1150955	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1150963	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11615961	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1259233	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1259235	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259236	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1259239	0.84[EUR][1000 genomes]
rs1259241	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1259353	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1259354	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1259355	0.81[ASN][1000 genomes]
rs1259356	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs1259359	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap]
rs1259386	0.91[CHB][hapmap]
rs1259405	0.82[CEU][hapmap]
rs1259409	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs1259422	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1259428	0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1259430	0.80[CEU][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259432	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1259435	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1259437	0.82[CEU][hapmap];0.93[CHB][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1259438	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1259441	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1262390	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1271128	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1271663	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1272773	0.82[CEU][hapmap];0.93[CHB][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1469673	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1677154	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1677173	0.83[ASN][1000 genomes]
rs1716216	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2061761	0.81[CEU][hapmap]
rs2116704	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2374190	0.85[CHB][hapmap]
rs2568884	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2568885	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2568887	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs2568888	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2617190	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2617191	0.91[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2617200	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682679	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2682686	0.81[EUR][1000 genomes]
rs2682695	0.82[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap]
rs2682697	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3844573	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3850965	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs3898368	0.93[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs4482118	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs4931501	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs4931507	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs6487992	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs708200	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs708209	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs708212	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs708217	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs7133082	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs7135856	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs7136476	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs71440988	0.85[ASN][1000 genomes]
rs7294574	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7302698	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7307616	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs7313118	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs793146	0.91[ASN][1000 genomes]
rs793148	0.82[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap]
rs793150	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs793158	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs793161	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs793171	0.91[CEU][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793173	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs793174	0.82[CEU][hapmap];0.93[CHB][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs793175	0.84[EUR][1000 genomes]
rs793176	1.00[CHB][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793177	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs793180	0.91[ASN][1000 genomes]
rs793184	0.96[ASN][1000 genomes]
rs793186	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap]
rs7954595	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs7959877	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7962896	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7974437	0.87[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs7975761	0.93[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7976644	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs899159	0.93[CHB][hapmap]
rs976874	0.81[AFR][1000 genomes];0.83[AMR][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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1012154	DENND5B	cis	cerebellum	SCAN
rs1012154	DENND5B	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31542400-31645000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:31562400-31644400	Weak transcription	Brain Substantia Nigra	brain
3	chr12:31567400-31635800	Weak transcription	Osteobl	bone
4	chr12:31567800-31642800	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:31572000-31631200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:31572000-31631200	Weak transcription	HSMMtube	muscle
7	chr12:31572400-31628400	Weak transcription	Right Ventricle	heart
8	chr12:31572400-31631200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:31577800-31649400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:31579000-31632000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:31579400-31632000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:31585000-31631600	Weak transcription	Brain Anterior Caudate	brain
14	chr12:31585000-31642000	Weak transcription	Fetal Kidney	kidney
15	chr12:31585400-31631800	Weak transcription	Fetal Lung	lung
16	chr12:31586200-31635800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:31594400-31648400	Weak transcription	Small Intestine	intestine
18	chr12:31600600-31630400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:31600600-31632000	Weak transcription	Brain Germinal Matrix	brain
20	chr12:31600800-31631600	Weak transcription	Adipose Nuclei	Adipose
21	chr12:31603800-31632600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:31605400-31630800	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:31605400-31631200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:31605400-31647200	Weak transcription	Psoas Muscle	Psoas
25	chr12:31605600-31632000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:31605600-31632200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:31605600-31637000	Weak transcription	Fetal Stomach	stomach
28	chr12:31607400-31631200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:31608600-31632000	Weak transcription	Placenta	Placenta
30	chr12:31610200-31632000	Weak transcription	Ovary	ovary
31	chr12:31613400-31631200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:31613400-31632000	Weak transcription	HSMM	muscle
33	chr12:31613600-31629400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:31615400-31632000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:31618200-31632200	Weak transcription	Aorta	Aorta
36	chr12:31619000-31632200	Weak transcription	Fetal Brain Female	brain
37	chr12:31619600-31635800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:31620000-31631200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:31620000-31635600	Weak transcription	HUVEC	blood vessel
40	chr12:31620200-31644800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:31620600-31631400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:31622400-31628600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:31622800-31629000	Weak transcription	GM12878-XiMat	blood
44	chr12:31623000-31635800	Weak transcription	NHEK	skin
45	chr12:31623800-31630200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:31624000-31628400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:31624200-31632200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:31624400-31629600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:31625200-31628400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr12:31625400-31628400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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