Variant report

Variant	rs62139608
Chromosome Location	chr2:30710976-30710977
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30703972..30706142-chr2:30708659..30711183,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10180482	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10201729	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10202174	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10495777	0.81[ASN][1000 genomes]
rs12053230	0.82[ASN][1000 genomes]
rs12993078	0.84[ASN][1000 genomes]
rs13014119	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13017224	0.94[ASN][1000 genomes]
rs13025287	0.83[ASN][1000 genomes]
rs13395754	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1357850	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525063	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17038632	0.83[ASN][1000 genomes]
rs28666424	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35116667	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs36072623	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56150357	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6705814	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6724421	0.92[EUR][1000 genomes]
rs6739322	0.83[ASN][1000 genomes]
rs894788	0.85[EUR][1000 genomes];0.84[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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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 target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62139608	LYCAT	cis	multi-tissue	Pritchard
rs62139608	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30697800-30720800	Weak transcription	Thymus	Thymus
2	chr2:30699000-30711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:30701200-30714400	Weak transcription	HSMM	muscle
4	chr2:30704600-30715800	Weak transcription	Psoas Muscle	Psoas
5	chr2:30704600-30719600	Weak transcription	Right Atrium	heart
6	chr2:30704600-30719800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:30704600-30720600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:30704800-30714200	Weak transcription	HSMMtube	muscle
9	chr2:30704800-30714400	Weak transcription	A549	lung
10	chr2:30705600-30711000	Weak transcription	Fetal Intestine Large	intestine
11	chr2:30705600-30711400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:30706000-30711000	Weak transcription	Small Intestine	intestine
13	chr2:30706400-30712200	Enhancers	Fetal Heart	heart
14	chr2:30707800-30715200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:30708000-30715400	Weak transcription	Primary B cells from cord blood	blood
16	chr2:30708200-30716000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:30709200-30711800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr2:30709400-30711600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:30709400-30712000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:30709600-30711600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr2:30709800-30715800	Weak transcription	Right Ventricle	heart
22	chr2:30710200-30711600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:30710400-30711000	Enhancers	Primary T cells from cord blood	blood
24	chr2:30710400-30711400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:30710400-30711400	Enhancers	NHDF-Ad	bronchial
26	chr2:30710400-30711600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:30710400-30711600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:30710400-30711600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:30710400-30711600	Enhancers	Fetal Kidney	kidney
30	chr2:30710400-30711800	Enhancers	Duodenum Mucosa	Duodenum
31	chr2:30710600-30711000	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:30710600-30711000	Enhancers	Osteobl	bone
33	chr2:30710600-30711200	Enhancers	Fetal Lung	lung
34	chr2:30710600-30711400	Enhancers	Primary T cells fromperipheralblood	blood
35	chr2:30710600-30711400	Enhancers	Left Ventricle	heart
36	chr2:30710600-30711400	Enhancers	Ovary	ovary
37	chr2:30710600-30711400	Enhancers	GM12878-XiMat	blood
38	chr2:30710600-30711400	Enhancers	HepG2	liver
39	chr2:30710600-30711400	Enhancers	NHLF	lung
40	chr2:30710600-30711600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:30710600-30711600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:30710600-30711600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr2:30710600-30711800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:30710600-30711800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr2:30710600-30715800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:30710800-30711200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr2:30710800-30711200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:30710800-30711600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr2:30710800-30715200	Weak transcription	Aorta	Aorta

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