Variant report

Variant	rs1662955
Chromosome Location	chr2:30670973-30670974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30454671..30456447-chr2:30669328..30672295,2	K562	blood:

Variant related genes	Relation type
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11686191	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892635	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1252639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252641	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252643	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252647	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1612616	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs1614348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1615605	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1662941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662958	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1723156	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1723167	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1723170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723175	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462562	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692041	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28538173	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35418935	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952124	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952148	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952151	0.80[MEX][hapmap]
rs72853154	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7562645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs829562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829570	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829573	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]
rs829576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829577	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829579	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[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];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829636	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829638	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829647	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829648	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829649	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829651	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829658	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829686	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829687	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829689	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829690	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829693	0.86[CEU][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1662955	LYCAT	cis	multi-tissue	Pritchard
rs1662955	LCLAT1	cis	cerebellum	SCAN
rs1662955	LYCAT	Cis_1M	lymphoblastoid	RTeQTL
rs1662955	LCLAT1	cis	Liver	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30669400-30671000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:30669400-30671200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr2:30669400-30671400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:30669400-30671400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:30669400-30671400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:30669400-30672000	Active TSS	Right Ventricle	heart
7	chr2:30669600-30671000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr2:30669600-30671000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:30669600-30671000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:30669600-30671000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:30669600-30671000	Active TSS	Aorta	Aorta
12	chr2:30669600-30671000	Active TSS	Ovary	ovary
13	chr2:30669600-30671000	Active TSS	Pancreas	Pancrea
14	chr2:30669600-30671200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr2:30669600-30671200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr2:30669600-30671200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:30669600-30671400	Active TSS	Left Ventricle	heart
18	chr2:30669600-30671400	Active TSS	NHDF-Ad	bronchial
19	chr2:30669800-30671000	Active TSS	Brain Hippocampus Middle	brain
20	chr2:30669800-30671000	Active TSS	Esophagus	oesophagus
21	chr2:30669800-30671000	Active TSS	A549	lung
22	chr2:30669800-30671200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:30669800-30671400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr2:30669800-30671400	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr2:30669800-30671400	Active TSS	Fetal Intestine Large	intestine
26	chr2:30669800-30671400	Active TSS	Lung	lung
27	chr2:30669800-30671600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:30669800-30671600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:30670000-30671000	Active TSS	Fetal Stomach	stomach
30	chr2:30670200-30671000	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr2:30670200-30671000	Flanking Active TSS	Placenta	Placenta
32	chr2:30670200-30671600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr2:30670400-30671000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:30670400-30671000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:30670400-30671000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr2:30670400-30671000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr2:30670400-30671000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:30670400-30671000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:30670400-30671000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:30670400-30671000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr2:30670400-30671000	Flanking Active TSS	Colonic Mucosa	Colon
42	chr2:30670400-30671000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr2:30670400-30671200	Flanking Active TSS	NH-A	brain
44	chr2:30670400-30671400	Flanking Active TSS	Liver	Liver
45	chr2:30670400-30671400	Flanking Active TSS	HMEC	breast
46	chr2:30670400-30671400	Flanking Active TSS	HUVEC	blood vessel
47	chr2:30670400-30671600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:30670600-30671000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
49	chr2:30670600-30671000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr2:30670600-30671000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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