Variant report

Variant	rs10784370
Chromosome Location	chr12:40497095-40497096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:40495644..40497821-chr12:40498343..40500336,2	MCF-7	breast:
2	chr12:40494859..40496427-chr12:40496570..40499467,2	MCF-7	breast:
3	chr11:62607295..62609623-chr12:40497021..40499693,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction
ENSG00000151229	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1031996	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10784381	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10784386	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10878113	0.81[EUR][1000 genomes]
rs1117378	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11175275	0.88[EUR][1000 genomes]
rs11175326	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11175327	0.80[EUR][1000 genomes]
rs12230710	0.80[EUR][1000 genomes]
rs1352876	0.85[CEU][hapmap]
rs1388589	0.88[EUR][1000 genomes]
rs1388590	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1472118	0.82[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1482284	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1482285	0.89[EUR][1000 genomes]
rs1482287	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1482288	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1491927	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1491931	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1844921	0.83[EUR][1000 genomes]
rs1844922	0.83[EUR][1000 genomes]
rs1873612	0.89[EUR][1000 genomes]
rs1905121	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1948380	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2170503	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2404573	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs2638231	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2638232	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2638245	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2638249	0.87[EUR][1000 genomes]
rs2638254	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2638257	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2638258	0.89[EUR][1000 genomes]
rs2638260	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2638262	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2638263	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2638264	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2638266	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2708449	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2708464	0.89[EUR][1000 genomes]
rs2708466	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708473	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2708474	0.88[EUR][1000 genomes]
rs2708480	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2708485	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2708491	0.85[EUR][1000 genomes]
rs2708492	0.85[EUR][1000 genomes]
rs2708493	0.82[EUR][1000 genomes]
rs2708494	0.82[CEU][hapmap];0.80[CHB][hapmap];0.81[EUR][1000 genomes]
rs3812791	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4360759	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs4363681	0.89[EUR][1000 genomes]
rs6581514	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6581519	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7132203	0.91[EUR][1000 genomes]
rs716231	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs716268	0.82[CHB][hapmap]
rs728622	0.87[EUR][1000 genomes]
rs728623	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729216	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7306140	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7310430	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs878010	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs900253	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs937109	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs937110	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs937111	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1816874	chr12:40492814-40499934	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
5	esv1822895	chr12:40492814-40499934	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
6	esv1838004	chr12:40492814-40499934	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
7	esv1841992	chr12:40492814-40499934	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
8	esv1850635	chr12:40492814-40499934	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
9	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1839896	chr12:40493591-40499908	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
12	esv1834762	chr12:40496733-40499934	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
13	esv1799112	chr12:40497095-40499908	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
14	esv1840625	chr12:40497095-40499908	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10784370	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL
rs10784370	AC079630.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40466400-40498200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40475400-40497200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:40476400-40497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:40476600-40498400	Weak transcription	Fetal Stomach	stomach
5	chr12:40476800-40497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:40482000-40497800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:40487000-40497400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:40488200-40498600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:40492400-40498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:40492800-40497600	Weak transcription	Left Ventricle	heart
11	chr12:40492800-40498000	Weak transcription	Gastric	stomach
12	chr12:40492800-40498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:40492800-40498600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:40492800-40498600	Weak transcription	Lung	lung
15	chr12:40493800-40497400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:40493800-40497400	Weak transcription	Fetal Heart	heart
17	chr12:40494200-40498000	Weak transcription	Fetal Lung	lung
18	chr12:40494200-40498200	Weak transcription	A549	lung
19	chr12:40494600-40498000	Weak transcription	NHLF	lung
20	chr12:40495200-40497400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr12:40495400-40498000	Enhancers	Small Intestine	intestine
22	chr12:40495800-40497600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:40495800-40497600	Enhancers	Colon Smooth Muscle	Colon
24	chr12:40496400-40497200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:40496400-40497800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:40496600-40497800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr12:40496800-40497200	Enhancers	Pancreas	Pancrea
28	chr12:40496800-40497200	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr12:40496800-40497200	Flanking Active TSS	K562	blood
30	chr12:40496800-40497400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:40496800-40497400	Enhancers	Fetal Intestine Small	intestine
32	chr12:40496800-40497600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr12:40496800-40497600	Enhancers	Fetal Intestine Large	intestine
34	chr12:40496800-40497800	Enhancers	HepG2	liver
35	chr12:40496800-40498400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:40496800-40498600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:40496800-40498600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:40496800-40499000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr12:40496800-40500400	Active TSS	Stomach Smooth Muscle	stomach
40	chr12:40496800-40501600	Active TSS	Brain Cingulate Gyrus	brain
41	chr12:40496800-40501600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:40496800-40501600	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr12:40497000-40497200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:40497000-40497200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr12:40497000-40497200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:40497000-40497200	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr12:40497000-40497200	Enhancers	Ovary	ovary
48	chr12:40497000-40497200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr12:40497000-40497400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:40497000-40497400	Flanking Active TSS	Brain Anterior Caudate	brain

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