Variant report

Variant	rs12872974
Chromosome Location	chr13:49664492-49664493
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49657055..49658682-chr13:49662572..49665462,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1359066	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407827	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1407829	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928109	0.83[EUR][1000 genomes]
rs1928110	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1937180	0.85[EUR][1000 genomes]
rs1937181	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983805	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2021622	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026029	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2146748	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2149498	0.85[EUR][1000 genomes]
rs2181537	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181538	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181539	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2183095	0.83[EUR][1000 genomes]
rs2224742	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2407265	0.85[EUR][1000 genomes]
rs2407266	0.83[EUR][1000 genomes]
rs2897633	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2987528	0.83[EUR][1000 genomes]
rs2987535	0.82[EUR][1000 genomes]
rs2994377	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2994378	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2994379	0.88[EUR][1000 genomes]
rs2994380	0.88[EUR][1000 genomes]
rs2994381	0.88[EUR][1000 genomes]
rs3012116	0.83[EUR][1000 genomes]
rs3012117	0.83[EUR][1000 genomes]
rs3012118	0.83[EUR][1000 genomes]
rs3012121	0.83[EUR][1000 genomes]
rs3012127	0.88[EUR][1000 genomes]
rs3012133	0.80[EUR][1000 genomes]
rs3012135	0.82[EUR][1000 genomes]
rs3012136	0.82[EUR][1000 genomes]
rs34360275	0.89[EUR][1000 genomes]
rs35018425	0.83[EUR][1000 genomes]
rs4142065	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4245350	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4530025	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4942795	0.82[EUR][1000 genomes]
rs4942796	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4942798	0.86[EUR][1000 genomes]
rs4942799	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4942800	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561491	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6561493	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561496	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6561497	0.88[ASN][1000 genomes]
rs6561504	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7139819	0.83[EUR][1000 genomes]
rs7139854	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs716722	0.82[EUR][1000 genomes]
rs728075	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7317908	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7318871	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328000	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7329291	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7331917	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7333097	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7333285	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7338529	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7983885	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7986624	0.86[EUR][1000 genomes]
rs7987258	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7988168	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7989175	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7990573	0.91[EUR][1000 genomes]
rs7994845	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7994910	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7995616	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7997118	0.84[EUR][1000 genomes]
rs7998359	0.83[EUR][1000 genomes]
rs7999513	0.85[EUR][1000 genomes]
rs9316426	0.85[EUR][1000 genomes]
rs9316428	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9316429	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9526517	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9526518	0.86[EUR][1000 genomes]
rs9526520	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9526521	0.83[EUR][1000 genomes]
rs9526525	0.80[EUR][1000 genomes]
rs9535126	0.82[EUR][1000 genomes]
rs9535133	0.86[EUR][1000 genomes]
rs9535136	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535140	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535141	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535145	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535146	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535147	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535149	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535154	0.90[EUR][1000 genomes]
rs9535155	0.80[EUR][1000 genomes]
rs9535156	0.84[EUR][1000 genomes]
rs9562866	0.86[EUR][1000 genomes]
rs9562870	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9568150	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568151	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568154	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9591235	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9596064	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv976274	chr13:49655803-49666815	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1035	chr13:49656225-49700371	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49627400-49672400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:49629000-49665600	Weak transcription	Lung	lung
3	chr13:49629600-49665400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr13:49632200-49664800	Weak transcription	Fetal Lung	lung
5	chr13:49636800-49667800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr13:49639600-49687200	Weak transcription	Pancreas	Pancrea
7	chr13:49640600-49683800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:49641800-49671600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr13:49645000-49671000	Weak transcription	Small Intestine	intestine
10	chr13:49649400-49684200	Weak transcription	Right Ventricle	heart
11	chr13:49649800-49671600	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:49651400-49665600	Weak transcription	Fetal Thymus	thymus
13	chr13:49651400-49666800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:49651600-49670200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:49651600-49670800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr13:49651800-49664800	Weak transcription	Fetal Stomach	stomach
17	chr13:49651800-49665000	Weak transcription	Fetal Muscle Leg	muscle
18	chr13:49651800-49671000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr13:49651800-49671800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr13:49651800-49684000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr13:49651800-49684000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr13:49652000-49667600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr13:49652000-49671000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr13:49652400-49671600	Weak transcription	Spleen	Spleen
25	chr13:49655200-49667400	Weak transcription	HepG2	liver
26	chr13:49655600-49684200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr13:49656000-49673000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr13:49657200-49671600	Weak transcription	Ovary	ovary
29	chr13:49657200-49672200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr13:49657200-49692400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:49657400-49665600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr13:49657400-49668200	Weak transcription	Thymus	Thymus
33	chr13:49657400-49670800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr13:49657400-49670800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr13:49657400-49670800	Weak transcription	Aorta	Aorta
36	chr13:49657400-49671200	Weak transcription	HSMM	muscle
37	chr13:49657400-49671600	Weak transcription	Left Ventricle	heart
38	chr13:49657400-49674800	Weak transcription	Fetal Intestine Large	intestine
39	chr13:49657400-49674800	Weak transcription	Placenta	Placenta
40	chr13:49657400-49684000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr13:49657600-49670200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:49657600-49670800	Weak transcription	Liver	Liver
43	chr13:49657800-49683800	Weak transcription	Primary B cells from cord blood	blood
44	chr13:49658000-49665600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:49658000-49671000	Weak transcription	HSMMtube	muscle
46	chr13:49658000-49671400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr13:49658800-49671600	Weak transcription	Colon Smooth Muscle	Colon
48	chr13:49659400-49666600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr13:49659400-49672800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr13:49659800-49669800	Weak transcription	GM12878-XiMat	blood

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