Variant report

Variant	rs17489631
Chromosome Location	chr12:40496733-40496734
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	chr12:40495644..40497821-chr12:40498343..40500336,2	MCF-7	breast:
2	chr12:40494859..40496427-chr12:40496570..40499467,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151229	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs58432263	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7316539	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

No data

Chromatin state (count:58 , 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	chr12:40471400-40496800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:40474400-40497000	Weak transcription	Ovary	ovary
4	chr12:40475400-40497200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:40476400-40497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:40476600-40498400	Weak transcription	Fetal Stomach	stomach
7	chr12:40476800-40497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:40477000-40497000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:40477400-40496800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:40480600-40496800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:40482000-40497800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:40485600-40496800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:40487000-40497400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr12:40488200-40498600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:40491000-40497000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:40492400-40498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:40492800-40496800	Weak transcription	Pancreas	Pancrea
18	chr12:40492800-40497600	Weak transcription	Left Ventricle	heart
19	chr12:40492800-40498000	Weak transcription	Gastric	stomach
20	chr12:40492800-40498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:40492800-40498600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:40492800-40498600	Weak transcription	Lung	lung
23	chr12:40493600-40496800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:40493600-40497000	Weak transcription	Brain Anterior Caudate	brain
25	chr12:40493600-40497000	Weak transcription	Fetal Kidney	kidney
26	chr12:40493800-40497400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:40493800-40497400	Weak transcription	Fetal Heart	heart
28	chr12:40494000-40496800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:40494000-40496800	Weak transcription	HepG2	liver
30	chr12:40494000-40497000	Weak transcription	Liver	Liver
31	chr12:40494000-40497000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:40494200-40496800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:40494200-40496800	Weak transcription	Fetal Intestine Small	intestine
34	chr12:40494200-40496800	Enhancers	K562	blood
35	chr12:40494200-40498000	Weak transcription	Fetal Lung	lung
36	chr12:40494200-40498200	Weak transcription	A549	lung
37	chr12:40494400-40496800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:40494400-40497000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:40494600-40496800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:40494600-40497000	Weak transcription	Stomach Mucosa	stomach
41	chr12:40494600-40498000	Weak transcription	NHLF	lung
42	chr12:40495200-40497400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr12:40495400-40497000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr12:40495400-40498000	Enhancers	Small Intestine	intestine
45	chr12:40495800-40496800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr12:40495800-40497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:40495800-40497000	Weak transcription	Hela-S3	cervix
48	chr12:40495800-40497600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:40495800-40497600	Enhancers	Colon Smooth Muscle	Colon
50	chr12:40496000-40496800	Enhancers	Cortex derived primary cultured neurospheres	brain

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