Variant report

Variant	rs829573
Chromosome Location	chr2:30682630-30682631
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30618142..30620784-chr2:30680796..30682766,2	K562	blood:
2	chr2:30677517..30682510-chr2:30682594..30687236,9	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11686191	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11892635	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1252639	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1252641	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1252643	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1252647	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1612616	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs1614348	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1615605	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1662941	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662942	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662944	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662949	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662955	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1662958	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1723156	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1723167	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1723170	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1723175	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2462562	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2692041	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28538173	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35418935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4952124	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4952148	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952151	0.80[MEX][hapmap]
rs72853154	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562645	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs829562	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829570	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829571	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829576	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829577	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829584	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs829623	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829636	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs829638	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829645	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829647	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829648	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829649	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829650	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829651	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829658	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs829686	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829687	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829689	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs829690	0.86[EUR][1000 genomes]
rs829693	0.86[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes];0.82[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	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
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs829573	LCLAT1	cis	Liver	GTEx
rs829573	LYCAT	cis	multi-tissue	Pritchard
rs829573	LCLAT1	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671000-30685200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:30671200-30688200	Weak transcription	HSMM	muscle
3	chr2:30671600-30683800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:30671600-30685600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:30671600-30688000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:30671600-30688200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:30671600-30694600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:30671600-30703400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:30672000-30684600	Weak transcription	Hela-S3	cervix
11	chr2:30672000-30686400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:30672000-30686800	Weak transcription	Dnd41	blood
13	chr2:30672000-30688000	Weak transcription	Fetal Lung	lung
14	chr2:30674200-30687400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:30677800-30683800	Enhancers	Fetal Heart	heart
16	chr2:30678200-30684200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr2:30678200-30684200	Weak transcription	A549	lung
18	chr2:30678400-30704200	Weak transcription	Fetal Stomach	stomach
19	chr2:30678600-30688000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:30678600-30703800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:30678600-30710600	Weak transcription	NHLF	lung
22	chr2:30678800-30687800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:30679000-30683600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:30679000-30684200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr2:30679200-30688000	Weak transcription	Pancreas	Pancrea
26	chr2:30679400-30688000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:30679600-30683600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:30679600-30685800	Weak transcription	Fetal Thymus	thymus
29	chr2:30679800-30683200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:30679800-30687400	Weak transcription	Fetal Kidney	kidney
31	chr2:30679800-30688000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:30680400-30686400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:30680400-30688000	Weak transcription	Thymus	Thymus
34	chr2:30680600-30688000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:30680600-30688000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:30680800-30684000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:30681000-30683200	Enhancers	Small Intestine	intestine
38	chr2:30681000-30685800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr2:30681200-30683200	Enhancers	Psoas Muscle	Psoas
40	chr2:30681400-30683600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr2:30681400-30688000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:30681600-30683600	Enhancers	Primary T cells from cord blood	blood
43	chr2:30681800-30683800	Enhancers	Ovary	ovary
44	chr2:30682000-30683200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:30682000-30683200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:30682000-30683400	Enhancers	Right Ventricle	heart
47	chr2:30682200-30685200	Weak transcription	Primary B cells from cord blood	blood
48	chr2:30682200-30686600	Weak transcription	HepG2	liver
49	chr2:30682200-30688000	Weak transcription	GM12878-XiMat	blood
50	chr2:30682400-30683600	Weak transcription	Lung	lung

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