Variant report

Variant	rs1259233
Chromosome Location	chr12:31646097-31646098
allele	A/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:
2	chr12:31645681..31648505-chr12:31649831..31652317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255867	Chromatin interaction
ENSG00000170456	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1012154	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11051456	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1150942	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150943	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150950	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1150953	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1150954	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150955	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150963	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259235	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1259241	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259352	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1259353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259354	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259356	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259359	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259386	0.91[ASN][1000 genomes]
rs1259389	0.85[ASN][1000 genomes]
rs1259395	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1259405	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259409	0.84[EUR][1000 genomes]
rs1259422	0.85[AFR][1000 genomes]
rs1259426	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259430	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1259432	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1259435	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259437	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259438	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259441	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1262390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1271128	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1271663	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1272773	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542536	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1677154	0.81[AFR][1000 genomes]
rs1677186	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1677187	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1677189	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1716194	0.82[ASN][1000 genomes]
rs1716216	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2061761	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568885	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568887	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2568888	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2568894	0.84[AMR][1000 genomes]
rs2568902	0.90[AMR][1000 genomes]
rs2604052	0.91[ASN][1000 genomes]
rs2617178	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617191	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2617200	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2682671	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682674	0.86[ASN][1000 genomes]
rs2682677	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682679	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682680	0.89[ASN][1000 genomes]
rs2682686	0.85[EUR][1000 genomes]
rs2682695	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4312145	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs708212	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs708215	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs708217	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs792871	0.84[AMR][1000 genomes]
rs792875	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs793148	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793149	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793150	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793158	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793161	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs793171	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs793173	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793175	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793176	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs793177	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793186	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793191	0.84[AMR][1000 genomes]
rs899159	0.91[ASN][1000 genomes]
rs976874	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	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
7	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
8	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:84 , 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	chr12:31594400-31648400	Weak transcription	Small Intestine	intestine
4	chr12:31605400-31647200	Weak transcription	Psoas Muscle	Psoas
5	chr12:31628800-31655800	Weak transcription	Gastric	stomach
6	chr12:31630400-31655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:31633000-31648800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:31633000-31651600	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:31633000-31652400	Weak transcription	Fetal Brain Female	brain
10	chr12:31633200-31647200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:31633200-31647200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:31633200-31647400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:31633200-31649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:31633200-31649600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:31633200-31652200	Weak transcription	Adipose Nuclei	Adipose
16	chr12:31636200-31647200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:31636200-31663000	Weak transcription	Aorta	Aorta
18	chr12:31637200-31646600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr12:31637600-31648800	Weak transcription	Fetal Stomach	stomach
20	chr12:31639000-31655800	Weak transcription	Left Ventricle	heart
21	chr12:31640600-31650400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:31641800-31649000	Strong transcription	Primary B cells from cord blood	blood
23	chr12:31642600-31670000	Weak transcription	Fetal Lung	lung
24	chr12:31642800-31647200	Weak transcription	Ovary	ovary
25	chr12:31643200-31646200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:31643200-31646600	Weak transcription	Liver	Liver
27	chr12:31643200-31647200	Weak transcription	GM12878-XiMat	blood
28	chr12:31643400-31647600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:31643600-31648400	Enhancers	Hela-S3	cervix
30	chr12:31643600-31658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:31644000-31646200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr12:31644000-31646200	Enhancers	Fetal Heart	heart
33	chr12:31644000-31646200	Enhancers	HMEC	breast
34	chr12:31644000-31647000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:31644000-31648000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:31644000-31648200	Strong transcription	HepG2	liver
37	chr12:31644200-31646200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:31644200-31646400	Flanking Active TSS	A549	lung
39	chr12:31644400-31646200	Enhancers	Brain Anterior Caudate	brain
40	chr12:31644400-31646200	Enhancers	Brain Substantia Nigra	brain
41	chr12:31644400-31646200	Enhancers	HSMM	muscle
42	chr12:31644400-31646200	Enhancers	HSMMtube	muscle
43	chr12:31644400-31659400	Weak transcription	Pancreas	Pancrea
44	chr12:31644600-31646200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:31644600-31646200	Enhancers	Colon Smooth Muscle	Colon
46	chr12:31644600-31646400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:31644800-31650000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:31645000-31646200	Enhancers	Brain Angular Gyrus	brain
49	chr12:31645000-31647800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:31645200-31646200	Enhancers	Brain Inferior Temporal Lobe	brain

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