Variant report

Variant	rs3741877
Chromosome Location	chr12:31539122-31539123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:31538969..31541517-chr12:31543740..31545415,2	K562	blood:
2	chr12:31538215..31540416-chr12:31540541..31543060,2	K562	blood:
3	chr12:31476167..31479158-chr12:31538248..31540610,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139146	Chromatin interaction
ENSG00000177340	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10771826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771830	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10771831	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10771833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771834	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10771835	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10771837	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843937	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843939	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843953	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10843954	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843957	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10843962	0.85[EUR][1000 genomes]
rs10843968	0.80[EUR][1000 genomes]
rs11051414	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11051417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051427	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11051428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11051440	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11051446	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11051454	0.82[EUR][1000 genomes]
rs11051461	0.82[EUR][1000 genomes]
rs11051467	0.96[CEU][hapmap];0.83[YRI][hapmap]
rs12371432	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1268747	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1560634	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16918740	0.80[EUR][1000 genomes]
rs1879385	0.82[EUR][1000 genomes]
rs2163730	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2351921	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2351922	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs2351923	0.85[EUR][1000 genomes]
rs2892638	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34498192	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3741878	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3803114	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3887250	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[YRI][hapmap]
rs3898712	0.85[EUR][1000 genomes]
rs3926419	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4930979	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4931499	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4931511	0.85[EUR][1000 genomes]
rs4931512	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4931513	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs61097018	0.85[EUR][1000 genomes]
rs61918606	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61930275	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6487990	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487991	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7132688	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs7136559	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7297507	0.82[EUR][1000 genomes]
rs7297997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299425	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7300106	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7301326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7302695	0.82[EUR][1000 genomes]
rs7307615	0.85[AMR][1000 genomes]
rs73080572	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7308202	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7313889	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7314404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7314739	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7960380	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs7963764	0.84[EUR][1000 genomes]
rs7978277	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3741877	FLJ13224	cis	cerebellum	SCAN
rs3741877	DENND5B	cis	cerebellum	SCAN
rs3741877	ERGIC2	cis	cerebellum	SCAN
rs3741877	DENND5B	cis	parietal	SCAN
rs3741877	YARS2	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31524400-31540200	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:31530800-31541400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:31531800-31539600	Weak transcription	HSMM	muscle
4	chr12:31534400-31540400	Weak transcription	Psoas Muscle	Psoas
5	chr12:31534800-31541800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:31535400-31541800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:31535600-31560600	Weak transcription	Osteobl	bone
8	chr12:31535800-31539400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:31535800-31544000	Weak transcription	Fetal Lung	lung
10	chr12:31536000-31540400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:31536000-31550600	Weak transcription	Right Ventricle	heart
12	chr12:31536400-31539800	Weak transcription	Hela-S3	cervix
13	chr12:31536400-31624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:31536600-31547000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:31536600-31577400	Weak transcription	Small Intestine	intestine
16	chr12:31536800-31539400	Weak transcription	GM12878-XiMat	blood
17	chr12:31536800-31540400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:31537000-31539200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:31537000-31539400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:31537000-31540200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:31537200-31539200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:31537200-31540400	Weak transcription	Fetal Stomach	stomach
23	chr12:31537200-31546400	Strong transcription	Fetal Intestine Large	intestine
24	chr12:31537200-31555600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr12:31537400-31541200	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:31537400-31545800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:31537400-31604800	Weak transcription	Spleen	Spleen
28	chr12:31537600-31541800	Weak transcription	Fetal Brain Male	brain
29	chr12:31537600-31544800	Strong transcription	Fetal Brain Female	brain
30	chr12:31537600-31580800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:31537800-31540200	Weak transcription	HepG2	liver
32	chr12:31537800-31572400	Weak transcription	Stomach Mucosa	stomach
33	chr12:31538000-31540800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:31538000-31540800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr12:31538000-31541800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:31538000-31544400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr12:31538000-31549800	Strong transcription	A549	lung
38	chr12:31538000-31555600	Strong transcription	Liver	Liver
39	chr12:31538200-31539200	Strong transcription	Brain Anterior Caudate	brain
40	chr12:31538200-31539400	Active TSS	H9 Cell Line	embryonic stem cell
41	chr12:31538200-31540000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:31538200-31540400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:31538200-31540400	Weak transcription	Fetal Kidney	kidney
44	chr12:31538200-31540800	Strong transcription	Aorta	Aorta
45	chr12:31538200-31541000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:31538200-31542600	Strong transcription	Left Ventricle	heart
47	chr12:31538200-31544600	Strong transcription	Adipose Nuclei	Adipose
48	chr12:31538200-31545400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:31538200-31548600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:31538400-31539400	Strong transcription	Ovary	ovary

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