Variant report

Variant	rs829645
Chromosome Location	chr2:30696720-30696721
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	chr2:30695977..30698368-chr2:30707146..30708719,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11686191	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892635	0.90[AMR][1000 genomes];0.96[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];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252641	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252643	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252647	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1612616	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs1614348	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];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1615605	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1662941	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662942	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662944	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662949	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662955	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]
rs1662958	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1723156	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1723167	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1723170	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462562	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28538173	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35418935	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952124	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[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];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72853154	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7562645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829570	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[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];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829573	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]
rs829576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829577	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829579	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829584	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];0.98[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];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829636	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829638	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829647	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829648	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829649	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829651	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829658	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829686	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829687	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829689	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829690	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829693	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.87[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
rs829645	LYCAT	cis	multi-tissue	Pritchard
rs829645	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671600-30703400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:30678400-30704200	Weak transcription	Fetal Stomach	stomach
4	chr2:30678600-30703800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:30678600-30710600	Weak transcription	NHLF	lung
6	chr2:30682400-30704400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:30688200-30697600	Weak transcription	Thymus	Thymus
8	chr2:30688200-30703400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:30688400-30697200	Weak transcription	Right Ventricle	heart
10	chr2:30688400-30703400	Weak transcription	K562	blood
11	chr2:30688400-30703800	Weak transcription	Left Ventricle	heart
12	chr2:30688400-30704200	Weak transcription	Aorta	Aorta
13	chr2:30688400-30704600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:30688600-30710000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:30693000-30697400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:30693200-30697800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:30693200-30702000	Weak transcription	Fetal Intestine Small	intestine
18	chr2:30693200-30702200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:30693600-30704000	Weak transcription	A549	lung
20	chr2:30693600-30704000	Weak transcription	HepG2	liver
21	chr2:30695000-30696800	Enhancers	Primary T cells from cord blood	blood
22	chr2:30695000-30699000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr2:30695200-30698000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr2:30695200-30707000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:30695400-30704400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:30695600-30703600	Weak transcription	GM12878-XiMat	blood
27	chr2:30695600-30704200	Weak transcription	Fetal Lung	lung
28	chr2:30695600-30705400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:30695800-30697000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:30695800-30697800	Weak transcription	Primary B cells from cord blood	blood
31	chr2:30695800-30698000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr2:30695800-30698600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:30695800-30704000	Weak transcription	NHDF-Ad	bronchial
34	chr2:30695800-30704400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:30695800-30706600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:30696000-30698000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:30696000-30701400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:30696000-30704200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:30696200-30710600	Weak transcription	Ovary	ovary
40	chr2:30696600-30696800	Enhancers	Fetal Kidney	kidney
41	chr2:30696600-30697200	Enhancers	Fetal Heart	heart
42	chr2:30696600-30703400	Weak transcription	Duodenum Mucosa	Duodenum

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