Variant report

Variant	rs12774401
Chromosome Location	chr10:116476408-116476409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116475010..116479006-chr10:116480936..116484073,4	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1005968	0.81[ASN][1000 genomes]
rs10490908	1.00[CHB][hapmap]
rs10787544	0.90[YRI][hapmap]
rs10885589	0.80[YRI][hapmap]
rs1109267	0.90[YRI][hapmap]
rs11196828	0.80[YRI][hapmap]
rs11196835	0.90[YRI][hapmap]
rs11196843	0.80[GIH][hapmap]
rs11196860	0.87[AFR][1000 genomes]
rs11196963	1.00[CHB][hapmap]
rs11593135	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs11597188	1.00[ASW][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs11598354	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12570718	0.84[GIH][hapmap];0.89[LWK][hapmap]
rs12761207	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12761991	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12763449	0.80[EUR][1000 genomes]
rs12763784	0.83[EUR][1000 genomes]
rs12775180	1.00[CHB][hapmap]
rs12776647	0.90[YRI][hapmap]
rs12783562	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17092542	1.00[CHB][hapmap]
rs17720374	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17721283	1.00[CHB][hapmap]
rs17794002	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17794346	1.00[CHB][hapmap]
rs1966384	1.00[CHB][hapmap]
rs35221652	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35736355	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35927479	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36021781	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4568917	0.84[GIH][hapmap];0.83[LWK][hapmap];0.90[YRI][hapmap]
rs4752099	0.98[GIH][hapmap]
rs7072356	1.00[CHB][hapmap]
rs7074729	1.00[CHB][hapmap]
rs7075888	1.00[CHB][hapmap]
rs7094072	1.00[CHB][hapmap]
rs719894	0.92[ASN][1000 genomes]
rs749649	1.00[CHB][hapmap]
rs7895551	1.00[CHB][hapmap]
rs7902647	0.83[EUR][1000 genomes]
rs7909566	1.00[CHB][hapmap]
rs7909657	1.00[CHB][hapmap]
rs7919367	0.83[EUR][1000 genomes]
rs7923295	1.00[CHB][hapmap]
rs808325	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1042170	chr10:116455043-116504871	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1046888	chr10:116455043-116505640	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1038822	chr10:116455647-116497204	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12774401	TRUB1	cis	parietal	SCAN
rs12774401	ABLIM1	cis	parietal	SCAN
rs12774401	TRUB1	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116471800-116476800	Weak transcription	Right Ventricle	heart
2	chr10:116472600-116477400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr10:116472800-116476800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:116473000-116478200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr10:116473600-116478800	Weak transcription	Fetal Intestine Large	intestine
6	chr10:116473800-116476600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr10:116474200-116482800	Weak transcription	Brain Angular Gyrus	brain
8	chr10:116474400-116478200	Weak transcription	Fetal Muscle Leg	muscle
9	chr10:116474400-116479000	Weak transcription	Pancreas	Pancrea
10	chr10:116474400-116479000	Weak transcription	Small Intestine	intestine
11	chr10:116474400-116480600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:116474400-116480800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:116474400-116482200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr10:116474400-116486200	Weak transcription	Lung	lung
15	chr10:116475000-116483400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:116475200-116476800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:116475200-116477400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr10:116475200-116480400	Weak transcription	HSMMtube	muscle
19	chr10:116475400-116476600	Weak transcription	Liver	Liver
20	chr10:116475400-116477200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr10:116475400-116477400	Enhancers	A549	lung
22	chr10:116475400-116478200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr10:116475400-116478200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:116475400-116478400	Weak transcription	Brain Hippocampus Middle	brain
25	chr10:116475400-116478600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr10:116475400-116479000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr10:116475400-116479000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr10:116475400-116480600	Weak transcription	Aorta	Aorta
29	chr10:116475400-116480800	Weak transcription	Gastric	stomach
30	chr10:116475600-116477000	Enhancers	Fetal Lung	lung
31	chr10:116475600-116477400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:116475600-116484600	Enhancers	Adipose Nuclei	Adipose
33	chr10:116475800-116476800	Weak transcription	Left Ventricle	heart
34	chr10:116475800-116476800	Enhancers	HUVEC	blood vessel
35	chr10:116475800-116478400	Weak transcription	Brain Substantia Nigra	brain
36	chr10:116475800-116478800	Weak transcription	Stomach Mucosa	stomach
37	chr10:116475800-116479000	Weak transcription	Brain Anterior Caudate	brain
38	chr10:116475800-116479400	Enhancers	Hela-S3	cervix
39	chr10:116475800-116480200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr10:116475800-116480600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr10:116476000-116476800	Enhancers	Fetal Heart	heart
42	chr10:116476000-116476800	Weak transcription	Right Atrium	heart
43	chr10:116476000-116477000	Weak transcription	NH-A	brain
44	chr10:116476000-116477200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr10:116476000-116477400	Enhancers	Primary hematopoietic stem cells	blood
46	chr10:116476000-116477600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:116476200-116483200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr10:116476400-116476800	Weak transcription	Psoas Muscle	Psoas

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