Variant report

Variant	rs12975576
Chromosome Location	chr19:38625946-38625947
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	chr19:38625391..38627747-chr19:38633636..38636533,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10460171	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083447	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460188	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976860	0.81[EUR][1000 genomes]
rs12982030	0.82[ASN][1000 genomes]
rs12984016	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984380	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12984864	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12985707	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1545039	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1962866	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2004981	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2010234	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2016074	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2116862	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2163817	0.93[EUR][1000 genomes]
rs2304132	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2382972	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2382973	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2569517	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332845	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs332846	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs332852	0.81[EUR][1000 genomes]
rs332854	0.87[EUR][1000 genomes]
rs332857	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332859	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332860	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs332861	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332862	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs332863	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34646932	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35467693	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35469521	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35972455	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3852910	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3852911	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802248	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803805	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803808	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67910767	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71337549	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7253312	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7253633	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258019	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8100956	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107385	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855617	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
2	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
3	chr19:38610800-38643600	Weak transcription	HepG2	liver
4	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:38611600-38626000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:38611600-38634400	Weak transcription	Stomach Mucosa	stomach
7	chr19:38611600-38634800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:38611600-38634800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr19:38611600-38641400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
11	chr19:38611800-38634600	Weak transcription	NH-A	brain
12	chr19:38611800-38642600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
14	chr19:38613400-38633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:38613400-38634400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr19:38613600-38634800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr19:38613800-38626000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:38613800-38629800	Weak transcription	Liver	Liver
19	chr19:38613800-38630000	Weak transcription	Brain Hippocampus Middle	brain
20	chr19:38613800-38633000	Weak transcription	Brain Angular Gyrus	brain
21	chr19:38613800-38633000	Weak transcription	Brain Substantia Nigra	brain
22	chr19:38613800-38633400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:38613800-38635600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:38613800-38636600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:38613800-38639000	Weak transcription	Left Ventricle	heart
26	chr19:38613800-38641800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:38613800-38643200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr19:38613800-38652200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:38613800-38652600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr19:38614000-38630200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:38614000-38634800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:38616000-38652600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr19:38616200-38641600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:38616600-38642000	Weak transcription	Dnd41	blood
35	chr19:38617000-38652000	Strong transcription	Fetal Intestine Small	intestine
36	chr19:38617800-38626400	Strong transcription	Osteobl	bone
37	chr19:38618200-38651000	Strong transcription	Fetal Intestine Large	intestine
38	chr19:38618400-38626600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:38619000-38626600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr19:38619000-38630800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr19:38619600-38647800	Strong transcription	Fetal Stomach	stomach
42	chr19:38620600-38626800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:38620800-38626200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:38620800-38626800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr19:38620800-38632600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:38621000-38627000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr19:38621000-38633800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr19:38621400-38629000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:38621600-38630400	Weak transcription	Ovary	ovary
50	chr19:38621600-38642800	Weak transcription	NHLF	lung

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