Variant report

Variant	rs12816170
Chromosome Location	chr12:31649001-31649002
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	chr12:31645308..31649621-chr12:31742506..31745309,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1038066	0.87[EUR][1000 genomes]
rs1269139	0.80[EUR][1000 genomes]
rs12809140	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12812075	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812141	1.00[ASN][1000 genomes]
rs12816386	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818749	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12819062	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12820294	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12821808	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822601	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825207	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12826193	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12831480	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17497517	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17497656	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17497998	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1879399	1.00[ASN][1000 genomes]
rs2126897	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34007930	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34094545	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34184789	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34271764	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34308937	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34450466	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585237	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34642866	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34667511	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34949976	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34955459	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34986122	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35029695	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193529	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35545963	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35567364	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35679974	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35692484	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850967	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4338625	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4930977	0.80[AMR][1000 genomes]
rs4930981	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4930983	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4931485	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931498	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931503	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931504	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931510	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4931518	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55635343	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55643034	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55771933	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56183451	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234529	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282720	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56327034	1.00[ASN][1000 genomes]
rs56409505	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66479670	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66520413	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66552209	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66597773	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66635949	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67415228	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67963293	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68030436	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455664	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs71455667	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71455668	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455669	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455670	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71455671	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73080503	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73084486	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73086471	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73088505	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73088597	0.81[AMR][1000 genomes];0.87[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	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
5	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
6	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
7	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	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	chr12:31577800-31649400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:31628800-31655800	Weak transcription	Gastric	stomach
4	chr12:31630400-31655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:31633000-31651600	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:31633000-31652400	Weak transcription	Fetal Brain Female	brain
7	chr12:31633200-31649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:31633200-31649600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:31633200-31652200	Weak transcription	Adipose Nuclei	Adipose
10	chr12:31636200-31663000	Weak transcription	Aorta	Aorta
11	chr12:31639000-31655800	Weak transcription	Left Ventricle	heart
12	chr12:31640600-31650400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:31642600-31670000	Weak transcription	Fetal Lung	lung
14	chr12:31643600-31658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:31644400-31659400	Weak transcription	Pancreas	Pancrea
16	chr12:31644800-31650000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:31645200-31650200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:31645400-31650000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:31645600-31658000	Weak transcription	Fetal Intestine Small	intestine
20	chr12:31645800-31649200	Weak transcription	NHDF-Ad	bronchial
21	chr12:31645800-31649400	Weak transcription	NHLF	lung
22	chr12:31645800-31650200	Weak transcription	Osteobl	bone
23	chr12:31645800-31651000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:31645800-31651000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:31646000-31649200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:31646000-31649800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:31646000-31650600	Weak transcription	Right Ventricle	heart
28	chr12:31646000-31651000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:31646000-31652000	Weak transcription	Brain Germinal Matrix	brain
30	chr12:31646000-31652400	Weak transcription	Fetal Kidney	kidney
31	chr12:31646000-31652600	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:31646000-31659400	Weak transcription	NH-A	brain
33	chr12:31646000-31659800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:31646200-31650200	Weak transcription	Fetal Heart	heart
35	chr12:31646200-31650600	Weak transcription	HSMM	muscle
36	chr12:31646200-31651000	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:31646200-31651200	Weak transcription	HUVEC	blood vessel
38	chr12:31646200-31651400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:31646200-31652600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:31646200-31657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:31646400-31649400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:31646600-31649200	Genic enhancers	A549	lung
43	chr12:31646800-31650200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:31647000-31652200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:31647400-31650400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:31647400-31660000	Weak transcription	Psoas Muscle	Psoas
47	chr12:31647600-31650200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr12:31647600-31650400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:31647600-31650400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:31647600-31650400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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