Variant report

Variant	rs10845540
Chromosome Location	chr12:12580224-12580225
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	chr12:12578734..12582406-chr12:12583548..12588483,5	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1019340	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1019341	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1030069	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10459098	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743985	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10772563	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10772566	0.82[ASN][1000 genomes]
rs10772567	0.82[ASN][1000 genomes]
rs10845533	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10845537	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10845539	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10845541	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10845542	0.82[ASN][1000 genomes]
rs10845544	0.82[ASN][1000 genomes]
rs10845545	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10845546	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11054894	0.86[ASN][1000 genomes]
rs11532310	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11561172	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11609375	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11829916	0.81[ASN][1000 genomes]
rs1468876	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1544682	0.82[ASN][1000 genomes]
rs2160586	0.82[ASN][1000 genomes]
rs2216264	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2417187	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3925170	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4390432	0.88[ASN][1000 genomes]
rs4488294	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4547192	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763825	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763826	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763829	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4763830	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56701819	0.83[ASN][1000 genomes]
rs56915387	0.83[ASN][1000 genomes]
rs60253266	0.81[ASN][1000 genomes]
rs61543155	0.82[ASN][1000 genomes]
rs6488526	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7295080	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7309503	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7311364	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7313825	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315626	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7953025	0.85[ASN][1000 genomes]
rs7954752	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7961703	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967038	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7967111	0.87[ASN][1000 genomes]
rs7967466	0.85[ASN][1000 genomes]
rs7969020	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7969252	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969270	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969849	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969984	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs879445	0.90[ASN][1000 genomes]
rs888200	0.82[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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12558000-12586000	Weak transcription	Pancreas	Pancrea
2	chr12:12565200-12585000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:12572600-12588400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:12577400-12582200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:12577400-12582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:12577600-12580600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:12577600-12583800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:12577800-12581800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr12:12577800-12584000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:12578200-12588600	Weak transcription	Primary B cells from cord blood	blood
11	chr12:12578400-12586600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:12578400-12588200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:12578600-12580800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:12578800-12581800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:12578800-12586200	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:12578800-12589200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:12579000-12580600	Weak transcription	HMEC	breast
18	chr12:12579000-12581000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:12579000-12582000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:12579000-12582400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:12579000-12583400	Weak transcription	NHLF	lung
22	chr12:12579000-12583800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:12579200-12581800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:12579200-12582000	Weak transcription	HSMMtube	muscle
25	chr12:12579200-12582000	Weak transcription	Osteobl	bone
26	chr12:12579200-12582600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:12579200-12582600	Weak transcription	HSMM	muscle
28	chr12:12579200-12585200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:12579400-12580400	Weak transcription	HepG2	liver
30	chr12:12579400-12582000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:12579400-12582200	Weak transcription	Fetal Lung	lung
32	chr12:12579400-12585000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:12579400-12587000	Weak transcription	Psoas Muscle	Psoas
34	chr12:12579600-12583800	Weak transcription	Fetal Stomach	stomach
35	chr12:12579600-12585200	Weak transcription	Stomach Mucosa	stomach
36	chr12:12579600-12586600	Weak transcription	Fetal Intestine Large	intestine
37	chr12:12580000-12580600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:12580000-12580600	Weak transcription	Aorta	Aorta
39	chr12:12580000-12582200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:12580000-12588600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:12580200-12583800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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