Variant report

Variant	rs1019341
Chromosome Location	chr12:12592438-12592439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12590405..12593794-chr12:12593958..12596387,3	MCF-7	breast:
2	chr12:12591338..12594027-chr12:12713055..12715643,2	K562	blood:
3	chr12:12586894..12590134-chr12:12591817..12594282,3	K562	blood:
4	chr12:12586017..12588316-chr12:12590751..12594080,4	MCF-7	breast:
5	chr12:12588493..12590525-chr12:12592316..12593920,2	MCF-7	breast:
6	chr12:12592228..12593763-chr12:12712417..12714613,2	MCF-7	breast:
7	chr12:12588163..12590134-chr12:12591817..12594282,2	K562	blood:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1019340	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1030069	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10459098	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743982	0.85[ASN][1000 genomes]
rs10743985	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772563	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772566	0.92[ASN][1000 genomes]
rs10772567	0.92[ASN][1000 genomes]
rs10845533	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845537	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845539	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845540	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10845541	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845542	0.92[ASN][1000 genomes]
rs10845544	0.92[ASN][1000 genomes]
rs10845545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845546	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054894	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11054914	0.83[EUR][1000 genomes]
rs11532310	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11561172	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11609375	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11829916	0.85[ASN][1000 genomes]
rs1468876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544682	0.92[ASN][1000 genomes]
rs2160586	0.92[ASN][1000 genomes]
rs2193269	0.81[ASN][1000 genomes]
rs2193270	0.81[ASN][1000 genomes]
rs2216264	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2417187	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28853875	0.81[ASN][1000 genomes]
rs35908046	0.81[EUR][1000 genomes]
rs3925170	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4390432	0.97[ASN][1000 genomes]
rs4488294	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4547192	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763825	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763826	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763829	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763830	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56089442	0.82[ASN][1000 genomes]
rs56701819	0.86[ASN][1000 genomes]
rs56796062	0.81[ASN][1000 genomes]
rs56915387	0.86[ASN][1000 genomes]
rs60253266	0.82[ASN][1000 genomes]
rs61543155	0.86[ASN][1000 genomes]
rs6488526	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7295080	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7300150	0.80[ASN][1000 genomes]
rs73061463	0.82[ASN][1000 genomes]
rs7309503	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310012	0.83[ASN][1000 genomes]
rs7311363	0.85[ASN][1000 genomes]
rs7311364	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312010	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7313825	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315626	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953025	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7954752	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961703	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7967038	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967111	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967466	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969020	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969252	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969270	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969849	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969984	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879445	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888200	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12582600-12595000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:12582600-12599400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:12582800-12592600	Weak transcription	NH-A	brain
4	chr12:12582800-12596400	Weak transcription	Spleen	Spleen
5	chr12:12583000-12594000	Weak transcription	HSMMtube	muscle
6	chr12:12584000-12598600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:12584200-12592800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr12:12584200-12593200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:12585400-12593200	Weak transcription	Small Intestine	intestine
10	chr12:12585600-12595200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:12585800-12595400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:12586000-12593200	Weak transcription	Liver	Liver
13	chr12:12586000-12594200	Weak transcription	Hela-S3	cervix
14	chr12:12586000-12595000	Weak transcription	Adipose Nuclei	Adipose
15	chr12:12586200-12595000	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:12586200-12595400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:12586600-12594200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:12586800-12594000	Weak transcription	Right Ventricle	heart
19	chr12:12587000-12592600	Weak transcription	Stomach Mucosa	stomach
20	chr12:12587000-12593800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:12587000-12594800	Weak transcription	Aorta	Aorta
22	chr12:12587000-12594800	Weak transcription	Esophagus	oesophagus
23	chr12:12587000-12594800	Weak transcription	Placenta	Placenta
24	chr12:12587200-12593200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:12587200-12593800	Weak transcription	Fetal Intestine Small	intestine
26	chr12:12587200-12594000	Weak transcription	Brain Angular Gyrus	brain
27	chr12:12587200-12594000	Weak transcription	Lung	lung
28	chr12:12587200-12594000	Weak transcription	Psoas Muscle	Psoas
29	chr12:12587200-12594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:12587200-12595200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:12587200-12596400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:12587200-12596400	Weak transcription	Gastric	stomach
33	chr12:12587400-12592600	Weak transcription	Thymus	Thymus
34	chr12:12587400-12593200	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:12587400-12593800	Weak transcription	Pancreas	Pancrea
36	chr12:12587400-12594000	Weak transcription	Brain Anterior Caudate	brain
37	chr12:12587400-12594200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:12587400-12594800	Weak transcription	NHLF	lung
39	chr12:12587400-12595000	Weak transcription	NHDF-Ad	bronchial
40	chr12:12587400-12595400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:12587400-12595400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:12587400-12595800	Weak transcription	Fetal Stomach	stomach
43	chr12:12587400-12600200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:12587400-12600200	Weak transcription	Ovary	ovary
45	chr12:12587600-12592600	Weak transcription	A549	lung
46	chr12:12587800-12593800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:12588000-12594200	Weak transcription	Fetal Intestine Large	intestine
48	chr12:12588000-12595800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:12588400-12594000	Weak transcription	Brain Substantia Nigra	brain
50	chr12:12588400-12595400	Weak transcription	Brain Inferior Temporal Lobe	brain

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