Variant report

Variant	rs61616163
Chromosome Location	chr12:50083100-50083101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50077862..50079872-chr12:50080970..50084621,3	K562	blood:
2	chr12:50076925..50079550-chr12:50081857..50084496,3	K562	blood:
3	chr12:50080406..50083815-chr12:50089731..50092749,3	MCF-7	breast:
4	chr12:50080143..50085132-chr12:50089232..50093203,6	K562	blood:
5	chr12:50019169..50021488-chr12:50082295..50084408,2	K562	blood:
6	chr12:50080608..50083488-chr12:50095334..50097821,2	MCF-7	breast:
7	chr12:50081616..50083290-chr12:50091244..50093003,2	K562	blood:
8	chr12:50067484..50070430-chr12:50082743..50084854,2	K562	blood:
9	chr12:50073227..50075348-chr12:50080508..50083212,2	MCF-7	breast:
10	chr12:50081825..50083464-chr12:50134248..50136444,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1049986	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10875964	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10875968	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169063	0.82[ASN][1000 genomes]
rs11169080	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169097	0.89[AMR][1000 genomes]
rs11169101	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169104	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169106	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169109	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169111	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169112	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169113	0.81[AMR][1000 genomes]
rs11169118	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169125	0.85[AMR][1000 genomes]
rs11169127	0.83[AMR][1000 genomes]
rs11169133	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169140	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11615488	0.97[ASN][1000 genomes]
rs11834380	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12296586	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12299505	0.83[AMR][1000 genomes]
rs12299513	0.83[AMR][1000 genomes]
rs12301824	0.90[ASN][1000 genomes]
rs12303310	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12304796	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12305460	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12308256	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12309940	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12310510	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12314795	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12315224	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12315791	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12316284	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12317646	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12321169	0.85[AMR][1000 genomes]
rs1470906	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1574326	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2336058	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2878532	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3887727	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4073998	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4133070	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4563	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4584654	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57191490	0.87[ASN][1000 genomes]
rs57342147	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57463238	0.81[AMR][1000 genomes]
rs58446833	0.83[AMR][1000 genomes]
rs59233136	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59849800	0.83[AMR][1000 genomes]
rs60121503	0.87[ASN][1000 genomes]
rs60402517	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61512987	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61620972	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61710637	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6580719	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7136052	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7137976	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7299002	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7299609	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7306877	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7309607	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312658	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7313738	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73305085	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73305098	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73306808	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73309030	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs74089182	0.87[ASN][1000 genomes]
rs7688	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7952734	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7952938	0.82[ASN][1000 genomes]
rs7954994	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7955586	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956089	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7956181	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7962645	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7962863	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963954	1.00[ASN][1000 genomes]
rs7967624	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7979262	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7979285	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7980979	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8626	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs897056	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9804749	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9804971	0.85[AMR][1000 genomes];0.84[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50068600-50083600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:50070000-50083400	Weak transcription	Brain Substantia Nigra	brain
3	chr12:50077000-50084600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:50077400-50086200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:50078000-50087600	Weak transcription	Placenta	Placenta
6	chr12:50078000-50091000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:50078200-50083400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:50078200-50083600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:50078400-50083200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:50078600-50083400	Weak transcription	Fetal Thymus	thymus
11	chr12:50078600-50090600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:50078600-50092200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:50078800-50083400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:50078800-50083600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:50078800-50083600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:50078800-50083600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:50078800-50083600	Weak transcription	Spleen	Spleen
18	chr12:50078800-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:50078800-50088200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:50078800-50088200	Weak transcription	HSMM	muscle
21	chr12:50078800-50091800	Weak transcription	NH-A	brain
22	chr12:50078800-50092400	Weak transcription	NHLF	lung
23	chr12:50079000-50083200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:50079000-50083200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:50079000-50088000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:50079000-50088000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:50079000-50092000	Weak transcription	Small Intestine	intestine
28	chr12:50079000-50096200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:50079200-50083600	Weak transcription	Brain Anterior Caudate	brain
30	chr12:50079200-50090600	Weak transcription	Ovary	ovary
31	chr12:50079200-50091000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:50079200-50092400	Weak transcription	Fetal Stomach	stomach
33	chr12:50079200-50092800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:50079400-50088000	Weak transcription	HSMMtube	muscle
35	chr12:50079400-50090600	Weak transcription	Psoas Muscle	Psoas
36	chr12:50080400-50084400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:50080800-50083200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr12:50080800-50083200	Weak transcription	Adipose Nuclei	Adipose
39	chr12:50080800-50084400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:50080800-50092800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr12:50081400-50083200	Weak transcription	Lung	lung
42	chr12:50081400-50083800	Enhancers	Brain Hippocampus Middle	brain
43	chr12:50081600-50083800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr12:50081600-50085600	Enhancers	Primary B cells from peripheral blood	blood
45	chr12:50081800-50083200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:50082000-50085200	Enhancers	Primary T cells from cord blood	blood
47	chr12:50082000-50088000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:50082000-50088200	Weak transcription	Osteobl	bone
49	chr12:50082000-50092800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:50082200-50083200	Weak transcription	Brain Cingulate Gyrus	brain

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