Variant report

Variant	rs1654008
Chromosome Location	chr12:31559865-31559866
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31558219..31560921-chr12:31742852..31744650,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10843946	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1259215	0.88[EUR][1000 genomes]
rs1259237	0.88[EUR][1000 genomes]
rs1259240	0.88[EUR][1000 genomes]
rs1267631	0.88[EUR][1000 genomes]
rs1271657	0.88[EUR][1000 genomes]
rs1798769	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1798781	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1798782	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1864912	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2568880	0.88[EUR][1000 genomes]
rs2568886	0.88[EUR][1000 genomes]
rs2568896	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2617179	0.88[EUR][1000 genomes]
rs2617189	0.88[EUR][1000 genomes]
rs2617192	0.88[EUR][1000 genomes]
rs2617194	0.88[EUR][1000 genomes]
rs2679488	0.88[EUR][1000 genomes]
rs2679502	0.88[EUR][1000 genomes]
rs2679503	0.88[EUR][1000 genomes]
rs2682675	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2682681	0.88[EUR][1000 genomes]
rs2682682	0.88[EUR][1000 genomes]
rs2682683	0.88[EUR][1000 genomes]
rs2682684	0.88[EUR][1000 genomes]
rs2682690	0.88[EUR][1000 genomes]
rs2682702	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2947175	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4931491	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67985192	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs708196	0.86[AFR][1000 genomes]
rs708198	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs708199	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs708201	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs708202	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs708207	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs708210	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs708211	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs708216	0.81[AFR][1000 genomes]
rs708218	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs708220	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7300482	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7302238	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7302818	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs792874	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs793147	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs793152	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs793159	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs793160	0.89[EUR][1000 genomes]
rs793164	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs793172	0.88[EUR][1000 genomes]
rs793178	0.88[EUR][1000 genomes]
rs793181	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs793183	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs793187	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs793188	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs793189	0.81[EUR][1000 genomes]
rs796963	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs811088	0.88[EUR][1000 genomes]
rs971294	0.82[EUR][1000 genomes]
rs973510	0.88[EUR][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

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31535600-31560600	Weak transcription	Osteobl	bone
2	chr12:31536400-31624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:31536600-31577400	Weak transcription	Small Intestine	intestine
4	chr12:31537400-31604800	Weak transcription	Spleen	Spleen
5	chr12:31537600-31580800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:31537800-31572400	Weak transcription	Stomach Mucosa	stomach
7	chr12:31538600-31563400	Weak transcription	Colonic Mucosa	Colon
8	chr12:31539800-31584800	Weak transcription	Fetal Heart	heart
9	chr12:31540400-31565200	Weak transcription	HUVEC	blood vessel
10	chr12:31540800-31563400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:31540800-31565400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:31540800-31572200	Weak transcription	Lung	lung
13	chr12:31540800-31573200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:31540800-31576800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:31542000-31578400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:31542200-31566000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:31542200-31583600	Weak transcription	Placenta	Placenta
18	chr12:31542400-31564600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:31542400-31565400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:31542400-31571200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:31542400-31645000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:31542600-31605800	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:31542800-31575400	Weak transcription	Fetal Brain Male	brain
24	chr12:31542800-31578800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:31544200-31579000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:31544400-31581400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:31544600-31584200	Weak transcription	Fetal Lung	lung
28	chr12:31544800-31565000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:31544800-31576200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:31545800-31560400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:31545800-31583600	Weak transcription	Psoas Muscle	Psoas
32	chr12:31548800-31566200	Weak transcription	Fetal Kidney	kidney
33	chr12:31549800-31561800	Weak transcription	Brain Angular Gyrus	brain
34	chr12:31549800-31618000	Weak transcription	Pancreas	Pancrea
35	chr12:31550800-31573200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:31551400-31561800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:31551600-31564800	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:31553000-31565000	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:31554800-31560400	Weak transcription	Left Ventricle	heart
40	chr12:31554800-31560600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:31554800-31560600	Weak transcription	Right Ventricle	heart
42	chr12:31555000-31560400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:31555000-31565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:31555200-31560200	Weak transcription	Brain Germinal Matrix	brain
45	chr12:31555200-31560400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:31555200-31561600	Weak transcription	Fetal Brain Female	brain
47	chr12:31555200-31566200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:31555400-31565000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:31555400-31565400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:31555600-31560400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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