Variant report

Variant	rs3741878
Chromosome Location	chr12:31632449-31632450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31628236..31630828-chr12:31631836..31633451,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256159	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10771826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10771830	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771831	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10771833	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771834	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771835	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10771837	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843937	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10843938	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10843939	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10843953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843954	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843962	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843966	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843968	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843969	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843971	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11051427	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11051428	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11051440	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051454	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11051461	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11051467	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11051472	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051476	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs1150949	0.84[ASN][1000 genomes]
rs12369701	0.88[ASN][1000 genomes]
rs12371432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259360	0.84[ASN][1000 genomes]
rs1268747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1560634	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1677193	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap]
rs16918740	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1879385	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2163730	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2351921	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2351922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2351923	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2892638	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34498192	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3741877	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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3850966	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3887250	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs3898712	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4931499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931511	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61097018	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61918606	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61930275	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6487990	0.84[EUR][1000 genomes]
rs6487991	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487995	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7132688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7136559	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297507	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7297997	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7299425	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7300106	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7301326	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7302695	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73080572	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7308202	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7313889	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7314404	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7314739	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7960380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7963764	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7978277	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3741878	DENND5B	cis	parietal	SCAN
rs3741878	ERGIC2	cis	cerebellum	SCAN
rs3741878	FLJ13224	cis	cerebellum	SCAN
rs3741878	YARS2	cis	cerebellum	SCAN
rs3741878	DENND5B	cis	cerebellum	SCAN

Chromatin state (count:80 , 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	chr12:31577800-31649400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:31585000-31642000	Weak transcription	Fetal Kidney	kidney
8	chr12:31586200-31635800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:31594400-31648400	Weak transcription	Small Intestine	intestine
10	chr12:31603800-31632600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:31605400-31647200	Weak transcription	Psoas Muscle	Psoas
12	chr12:31605600-31637000	Weak transcription	Fetal Stomach	stomach
13	chr12:31619600-31635800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:31620000-31635600	Weak transcription	HUVEC	blood vessel
15	chr12:31620200-31644800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:31623000-31635800	Weak transcription	NHEK	skin
17	chr12:31625400-31636200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:31627600-31632800	Enhancers	Liver	Liver
19	chr12:31627600-31638800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:31628600-31634200	Weak transcription	Right Atrium	heart
21	chr12:31628800-31643400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:31628800-31644200	Weak transcription	Pancreas	Pancrea
23	chr12:31628800-31655800	Weak transcription	Gastric	stomach
24	chr12:31629000-31645000	Weak transcription	Brain Angular Gyrus	brain
25	chr12:31629400-31633200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:31629600-31633600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:31630200-31633200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:31630200-31633200	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr12:31630400-31632600	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:31630400-31633000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:31630400-31655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:31630800-31632600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:31630800-31633000	Strong transcription	Fetal Muscle Leg	muscle
34	chr12:31630800-31638800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:31631000-31633200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr12:31631200-31632800	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr12:31631200-31633000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:31631200-31633000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:31631200-31633000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:31631200-31633000	Strong transcription	HSMMtube	muscle
41	chr12:31631200-31633200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:31631400-31632600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:31631400-31633000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:31631400-31633000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:31631400-31633200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:31631400-31633200	Strong transcription	Fetal Intestine Large	intestine
47	chr12:31631400-31634200	Weak transcription	Lung	lung
48	chr12:31631600-31633000	Strong transcription	Brain Anterior Caudate	brain
49	chr12:31631600-31633200	Strong transcription	Adipose Nuclei	Adipose
50	chr12:31631600-31633400	Genic enhancers	A549	lung

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