Variant report

Variant	rs1252647
Chromosome Location	chr2:30742514-30742515
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	chr2:30740997..30743225-chr2:30749540..30752188,2	MCF-7	breast:
2	chr2:30739882..30742523-chr2:30744802..30747234,2	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	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11892635	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252639	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252641	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252643	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1614348	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1662941	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662942	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662944	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662949	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662955	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662958	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1723156	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1723167	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1723170	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1723175	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462562	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2692041	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28538173	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35418935	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952124	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952148	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72853154	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7562645	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829562	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829570	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829571	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829573	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs829576	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829577	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829579	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829584	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829623	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829636	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829638	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829645	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829647	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829648	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829649	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829650	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829651	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829658	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829686	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829687	0.85[AMR][1000 genomes];0.88[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
rs1252647	LYCAT	cis	multi-tissue	Pritchard
rs1252647	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30726200-30742600	Weak transcription	Pancreas	Pancrea
2	chr2:30729000-30764600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:30733000-30756000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:30734800-30764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:30735000-30742600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:30735000-30742600	Weak transcription	HSMMtube	muscle
7	chr2:30735400-30742600	Weak transcription	Fetal Intestine Large	intestine
8	chr2:30735600-30742800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:30736800-30752400	Weak transcription	Psoas Muscle	Psoas
10	chr2:30737800-30742600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:30738000-30742600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:30738000-30742600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:30738000-30742600	Weak transcription	NHEK	skin
14	chr2:30738000-30750400	Weak transcription	Liver	Liver
15	chr2:30738000-30757000	Weak transcription	Ovary	ovary
16	chr2:30738200-30742600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:30738200-30742600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:30738200-30742600	Weak transcription	NHLF	lung
19	chr2:30738200-30742800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:30738200-30744000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:30738200-30750000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:30738200-30750800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:30738200-30750800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:30738200-30751000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:30738200-30752400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:30738200-30758200	Weak transcription	Right Ventricle	heart
27	chr2:30738400-30748600	Weak transcription	Fetal Kidney	kidney
28	chr2:30738400-30756200	Weak transcription	Hela-S3	cervix
29	chr2:30740200-30742600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:30741000-30745200	Weak transcription	Fetal Heart	heart
31	chr2:30741200-30743000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
32	chr2:30741400-30743000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:30741400-30743000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:30741400-30743400	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr2:30741400-30743400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:30741400-30743600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:30741400-30744200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:30741600-30742800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
39	chr2:30741600-30743000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:30741600-30743200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
41	chr2:30741600-30743200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
42	chr2:30741600-30743200	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr2:30741600-30743200	ZNF genes & repeats	Fetal Thymus	thymus
44	chr2:30741600-30743600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
45	chr2:30741600-30744000	ZNF genes & repeats	Thymus	Thymus
46	chr2:30741800-30742600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:30741800-30742800	ZNF genes & repeats	Primary B cells from cord blood	blood
48	chr2:30741800-30743000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:30741800-30743000	ZNF genes & repeats	Fetal Muscle Leg	muscle
50	chr2:30741800-30743200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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