Variant report

Variant	rs1525063
Chromosome Location	chr2:30704945-30704946
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	chr2:30704716..30706255-chr2:30708517..30710606,2	MCF-7	breast:
2	chr2:30703972..30706142-chr2:30708659..30711183,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10180482	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10201729	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10202174	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10495777	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11127282	0.85[CHB][hapmap]
rs12052260	0.89[JPT][hapmap]
rs12052683	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs12053230	0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12613783	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12993078	0.82[ASN][1000 genomes]
rs12993664	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs13014119	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13017224	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs13025287	0.82[ASN][1000 genomes]
rs13395754	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1357850	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17038632	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs28666424	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35116667	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs36072623	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56150357	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62139608	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6705814	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6724421	0.88[EUR][1000 genomes]
rs6739322	0.84[ASN][1000 genomes]
rs829628	0.82[CHB][hapmap]
rs894788	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs958580	0.84[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1525063	LCLAT1	cis	cerebellum	SCAN
rs1525063	LYCAT	Cis_1M	lymphoblastoid	RTeQTL
rs1525063	LYCAT	cis	multi-tissue	Pritchard
rs1525063	EMILIN1	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30678600-30710600	Weak transcription	NHLF	lung
2	chr2:30688600-30710000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:30695200-30707000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:30695600-30705400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:30695800-30706600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:30696200-30710600	Weak transcription	Ovary	ovary
7	chr2:30697400-30710400	Weak transcription	Fetal Kidney	kidney
8	chr2:30697800-30720800	Weak transcription	Thymus	Thymus
9	chr2:30698000-30708000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:30698000-30709400	Weak transcription	Pancreas	Pancrea
11	chr2:30698200-30710600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:30698400-30706800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:30699000-30709600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:30699000-30711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:30699600-30709400	Weak transcription	Right Ventricle	heart
16	chr2:30701200-30705600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:30701200-30714400	Weak transcription	HSMM	muscle
18	chr2:30702800-30710400	Weak transcription	Primary T cells from cord blood	blood
19	chr2:30703600-30705000	Enhancers	GM12878-XiMat	blood
20	chr2:30703600-30706000	Enhancers	Fetal Heart	heart
21	chr2:30703600-30706000	Enhancers	Small Intestine	intestine
22	chr2:30704200-30705000	Enhancers	Fetal Lung	lung
23	chr2:30704200-30705000	Enhancers	Osteobl	bone
24	chr2:30704200-30705600	Enhancers	Fetal Stomach	stomach
25	chr2:30704200-30705800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:30704200-30705800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:30704200-30706000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:30704200-30706000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr2:30704400-30705000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:30704400-30705000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:30704400-30705000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:30704400-30705400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:30704400-30705600	Enhancers	Stomach Smooth Muscle	stomach
34	chr2:30704400-30706200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr2:30704600-30705000	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr2:30704600-30705200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr2:30704600-30705400	Weak transcription	Fetal Intestine Large	intestine
38	chr2:30704600-30705600	Weak transcription	Fetal Intestine Small	intestine
39	chr2:30704600-30706600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:30704600-30707000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:30704600-30709400	Weak transcription	Left Ventricle	heart
42	chr2:30704600-30710600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:30704600-30710600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:30704600-30715800	Weak transcription	Psoas Muscle	Psoas
45	chr2:30704600-30719600	Weak transcription	Right Atrium	heart
46	chr2:30704600-30719800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:30704600-30720600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:30704800-30705200	Weak transcription	Aorta	Aorta
49	chr2:30704800-30705200	Enhancers	Duodenum Mucosa	Duodenum
50	chr2:30704800-30705800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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