Variant report

Variant	rs829571
Chromosome Location	chr2:30683730-30683731
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	chr2:30677517..30682510-chr2:30682594..30687236,9	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11686191	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892635	0.92[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];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252641	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252643	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252647	0.83[AMR][1000 genomes];0.89[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1615605	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1662941	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662942	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662944	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662949	1.00[AFR][1000 genomes];0.97[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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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];1.00[AMR][1000 genomes];0.99[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];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1723170	1.00[AFR][1000 genomes];0.97[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];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462562	0.98[AFR][1000 genomes];0.97[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];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28538173	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35418935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72853154	0.88[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];0.81[AMR][1000 genomes];0.88[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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829570	1.00[AFR][1000 genomes];0.99[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];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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829577	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.82[AMR][1000 genomes];0.88[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];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829638	0.86[AMR][1000 genomes];0.89[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829647	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829648	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829649	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829651	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829658	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829686	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829687	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829689	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829690	0.86[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: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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs829571	LYCAT	Cis_1M	lymphoblastoid	RTeQTL
rs829571	LYCAT	cis	multi-tissue	Pritchard

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	chr2:30679000-30684200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr2:30679200-30688000	Weak transcription	Pancreas	Pancrea
25	chr2:30679400-30688000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:30679600-30685800	Weak transcription	Fetal Thymus	thymus
27	chr2:30679800-30687400	Weak transcription	Fetal Kidney	kidney
28	chr2:30679800-30688000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:30680400-30686400	Weak transcription	Fetal Intestine Small	intestine
30	chr2:30680400-30688000	Weak transcription	Thymus	Thymus
31	chr2:30680600-30688000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:30680600-30688000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:30680800-30684000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr2:30681000-30685800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr2:30681400-30688000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:30681800-30683800	Enhancers	Ovary	ovary
37	chr2:30682200-30685200	Weak transcription	Primary B cells from cord blood	blood
38	chr2:30682200-30686600	Weak transcription	HepG2	liver
39	chr2:30682200-30688000	Weak transcription	GM12878-XiMat	blood
40	chr2:30682400-30687400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:30682400-30687800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:30682400-30688000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:30682400-30688000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:30682400-30688000	Weak transcription	Fetal Intestine Large	intestine
45	chr2:30682400-30688000	Weak transcription	Right Atrium	heart
46	chr2:30682400-30693400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:30682400-30704400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:30682600-30685000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr2:30682600-30685200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:30682600-30686200	Weak transcription	Spleen	Spleen

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