Variant report

Variant	rs829658
Chromosome Location	chr2:30728359-30728360
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30727663..30729408-chr2:30731919..30733785,2	K562	blood:
2	chr2:30727521..30729274-chr2:30737533..30740125,3	K562	blood:
3	chr2:30719917..30724610-chr2:30726684..30729828,4	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11686191	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11892635	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252639	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252641	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252643	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252647	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1614348	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1662941	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1662942	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1662944	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662949	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662955	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662958	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1723156	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1723167	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1723170	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1723175	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2462562	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2692041	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28538173	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35418935	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4952124	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4952148	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72853154	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7562645	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829562	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829570	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829571	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829573	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs829576	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829577	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829579	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829584	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829623	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829636	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829638	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829645	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829647	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829648	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829649	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829650	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829651	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs829686	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829687	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[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
rs829658	LYCAT	cis	multi-tissue	Pritchard
rs829658	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30715600-30732800	Weak transcription	Hela-S3	cervix
2	chr2:30721400-30728400	Weak transcription	Liver	Liver
3	chr2:30721400-30739000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:30724000-30732600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:30724200-30728400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr2:30724200-30728400	Weak transcription	K562	blood
7	chr2:30724200-30733400	Weak transcription	Fetal Intestine Large	intestine
8	chr2:30724200-30733800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:30724200-30734000	Weak transcription	Ovary	ovary
10	chr2:30724200-30737400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:30724600-30737400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:30725200-30729000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:30725200-30729000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:30725200-30729000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:30725400-30729000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:30725400-30729000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:30725600-30728800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:30725600-30729000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:30725600-30729000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:30725600-30729400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr2:30725800-30728800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:30726000-30728800	Enhancers	Fetal Lung	lung
23	chr2:30726200-30732400	Weak transcription	Left Ventricle	heart
24	chr2:30726200-30734200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:30726200-30742600	Weak transcription	Pancreas	Pancrea
26	chr2:30726400-30730000	Enhancers	Fetal Heart	heart
27	chr2:30726400-30733400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:30726400-30733800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:30726400-30734200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:30726600-30729000	Enhancers	Primary B cells from peripheral blood	blood
31	chr2:30726600-30737000	Weak transcription	Stomach Mucosa	stomach
32	chr2:30726800-30729000	Enhancers	Primary T cells from cord blood	blood
33	chr2:30726800-30729400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:30726800-30729600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr2:30727000-30728800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr2:30727000-30734400	Weak transcription	Psoas Muscle	Psoas
37	chr2:30727400-30728400	Enhancers	GM12878-XiMat	blood
38	chr2:30727400-30728800	Enhancers	NHLF	lung
39	chr2:30727600-30729000	Enhancers	Small Intestine	intestine
40	chr2:30727800-30732600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:30727800-30732800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:30727800-30734000	Weak transcription	Right Atrium	heart
43	chr2:30727800-30741400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:30728000-30728600	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr2:30728000-30729000	Enhancers	A549	lung
46	chr2:30728000-30729800	Enhancers	HepG2	liver
47	chr2:30728000-30739200	Weak transcription	Thymus	Thymus
48	chr2:30728200-30728800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:30728200-30728800	Enhancers	Primary B cells from cord blood	blood
50	chr2:30728200-30732800	Weak transcription	NHDF-Ad	bronchial

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