Variant report

Variant	rs16983601
Chromosome Location	chr19:52733977-52733978
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	chr19:52692325..52695090-chr19:52733176..52735417,3	MCF-7	breast:
2	chr19:52733004..52735653-chr19:52772074..52774471,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105568	Chromatin interaction
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10402209	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402638	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403154	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10403283	0.98[ASN][1000 genomes]
rs10403311	0.87[ASN][1000 genomes]
rs10403806	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404236	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10404437	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407063	0.98[ASN][1000 genomes]
rs10407502	0.96[ASN][1000 genomes]
rs10408119	0.98[ASN][1000 genomes]
rs10411211	0.98[ASN][1000 genomes]
rs10412110	0.98[ASN][1000 genomes]
rs10412196	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10413012	0.98[ASN][1000 genomes]
rs10414083	0.98[ASN][1000 genomes]
rs10414197	1.00[ASN][1000 genomes]
rs10414423	0.98[ASN][1000 genomes]
rs10414536	0.98[ASN][1000 genomes]
rs10414852	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416785	0.98[ASN][1000 genomes]
rs10417033	0.98[ASN][1000 genomes]
rs10417253	0.96[ASN][1000 genomes]
rs10417820	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418666	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10419304	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10420207	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10420254	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10420560	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420874	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10421589	0.87[ASN][1000 genomes]
rs10422838	0.98[ASN][1000 genomes]
rs10423125	0.87[ASN][1000 genomes]
rs10425135	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426002	0.98[ASN][1000 genomes]
rs10426786	0.98[ASN][1000 genomes]
rs1056348	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11879419	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16983598	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16983603	0.98[ASN][1000 genomes]
rs16983610	0.98[ASN][1000 genomes]
rs2115074	0.96[ASN][1000 genomes]
rs2288409	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2288410	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2303685	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28444225	0.94[ASN][1000 genomes]
rs28563055	0.94[ASN][1000 genomes]
rs3745097	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4458121	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55751302	0.98[ASN][1000 genomes]
rs55871532	0.98[ASN][1000 genomes]
rs57102373	0.98[ASN][1000 genomes]
rs60063830	0.98[ASN][1000 genomes]
rs6509628	0.96[ASN][1000 genomes]
rs7249460	0.98[ASN][1000 genomes]
rs7252174	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7254030	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7254774	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7255058	0.94[ASN][1000 genomes]
rs7255677	0.82[ASN][1000 genomes]
rs7255737	0.96[ASN][1000 genomes]
rs7256125	0.94[ASN][1000 genomes]
rs7256216	0.94[ASN][1000 genomes]
rs7256300	0.94[ASN][1000 genomes]
rs7256312	0.94[ASN][1000 genomes]
rs7256719	0.94[ASN][1000 genomes]
rs7259175	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73935052	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935053	0.98[ASN][1000 genomes]
rs755531	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8100048	0.94[ASN][1000 genomes]
rs8105432	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105792	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8106544	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8108636	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109061	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109512	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110857	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110881	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv962989	chr19:52732337-52742183	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52703000-52734600	Strong transcription	Fetal Stomach	stomach
2	chr19:52703200-52734000	Strong transcription	Lung	lung
3	chr19:52705000-52735200	Strong transcription	Stomach Smooth Muscle	stomach
4	chr19:52718000-52734200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:52719000-52735400	ZNF genes & repeats	A549	lung
6	chr19:52723600-52735200	Strong transcription	Fetal Muscle Leg	muscle
7	chr19:52727600-52737800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:52730200-52734400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:52730200-52737800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:52730400-52734000	Weak transcription	Small Intestine	intestine
11	chr19:52730800-52741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:52731000-52736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:52731000-52736800	Weak transcription	Stomach Mucosa	stomach
14	chr19:52731200-52734400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:52731600-52734600	Weak transcription	Aorta	Aorta
16	chr19:52731600-52736400	Weak transcription	Fetal Heart	heart
17	chr19:52731600-52738000	Weak transcription	Fetal Brain Male	brain
18	chr19:52731600-52741000	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:52731800-52735400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:52731800-52736600	Weak transcription	HUVEC	blood vessel
21	chr19:52732000-52734400	Weak transcription	NHDF-Ad	bronchial
22	chr19:52732000-52736000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:52732000-52736000	Weak transcription	Psoas Muscle	Psoas
24	chr19:52732000-52736600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr19:52732000-52740600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:52732000-52740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:52732200-52734000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:52732200-52734000	Weak transcription	NH-A	brain
29	chr19:52732200-52734200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:52732200-52734400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:52732200-52734400	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:52732200-52734600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:52732200-52735600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:52732200-52736000	Weak transcription	Ovary	ovary
35	chr19:52732200-52736000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr19:52732200-52736200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:52732200-52736400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:52732200-52741000	Weak transcription	Dnd41	blood
39	chr19:52732200-52741200	Weak transcription	Fetal Lung	lung
40	chr19:52732400-52734000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr19:52732400-52734000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:52732400-52734000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr19:52732400-52734000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:52732400-52734000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr19:52732400-52734000	Weak transcription	Fetal Thymus	thymus
46	chr19:52732400-52734000	Weak transcription	Pancreas	Pancrea
47	chr19:52732400-52734000	Weak transcription	Right Ventricle	heart
48	chr19:52732400-52734200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:52732400-52734200	Weak transcription	Brain Anterior Caudate	brain
50	chr19:52732400-52734200	Weak transcription	Gastric	stomach

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