Variant report

Variant	rs829664
Chromosome Location	chr2:30725733-30725734
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	chr2:30725140..30726941-chr2:30735622..30737355,2	K562	blood:
2	chr2:30716357..30718643-chr2:30723670..30726399,2	K562	blood:

Extended variants
information (count: 141 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10167083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175399	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs10183928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10865520	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1096109	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127278	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12053428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1252625	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs1252631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252640	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252646	0.92[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs1252651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1252654	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1447186	0.88[EUR][1000 genomes]
rs1447187	0.88[EUR][1000 genomes]
rs1470533	0.87[EUR][1000 genomes]
rs1470534	0.88[EUR][1000 genomes]
rs1470536	0.88[EUR][1000 genomes]
rs1525062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662946	0.81[EUR][1000 genomes]
rs17009647	1.00[YRI][hapmap]
rs17009802	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs17009815	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs1869423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869429	0.87[EUR][1000 genomes]
rs1975555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2121600	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2123753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2266377	0.81[EUR][1000 genomes]
rs2593440	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2593443	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2593448	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2593452	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593455	0.96[EUR][1000 genomes]
rs2593458	0.88[EUR][1000 genomes]
rs2593459	0.86[EUR][1000 genomes]
rs2593460	0.88[EUR][1000 genomes]
rs2593461	0.88[EUR][1000 genomes]
rs2593462	0.88[EUR][1000 genomes]
rs2593464	0.87[EUR][1000 genomes]
rs2593465	0.87[EUR][1000 genomes]
rs2593466	0.88[EUR][1000 genomes]
rs2593474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602780	0.87[EUR][1000 genomes]
rs2602782	0.86[EUR][1000 genomes]
rs2602783	0.88[EUR][1000 genomes]
rs2602784	0.88[EUR][1000 genomes]
rs2602785	0.88[EUR][1000 genomes]
rs2602786	0.88[EUR][1000 genomes]
rs2602789	0.86[EUR][1000 genomes]
rs2602790	0.88[EUR][1000 genomes]
rs2602791	0.88[EUR][1000 genomes]
rs2602792	0.88[EUR][1000 genomes]
rs2602798	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602799	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602806	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602807	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609924	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609925	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609926	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609943	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609945	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2609950	0.84[EUR][1000 genomes]
rs2609952	0.88[EUR][1000 genomes]
rs2609955	0.88[EUR][1000 genomes]
rs2609956	0.88[EUR][1000 genomes]
rs2609958	0.88[EUR][1000 genomes]
rs3862977	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952147	0.92[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs59120669	0.82[AFR][1000 genomes]
rs6718986	1.00[YRI][hapmap]
rs6731031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6740440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6759011	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6761612	1.00[YRI][hapmap]
rs72856691	0.81[AFR][1000 genomes]
rs72858915	0.82[AFR][1000 genomes]
rs7566983	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572318	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7583211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7591110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7592355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7605994	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7606200	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829563	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs829564	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs829565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs829574	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829575	0.92[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs829581	0.83[EUR][1000 genomes]
rs829582	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829616	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829617	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829618	0.92[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829619	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829620	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829622	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs829629	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829631	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829634	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs829635	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829637	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829639	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs829641	0.92[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs829642	0.85[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829646	0.85[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829653	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs829654	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs829655	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829659	0.85[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829660	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829661	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829669	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs829671	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829672	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829673	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829675	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829677	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs829679	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs829680	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs829682	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs829684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs829695	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs829696	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap]
rs829699	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs844194	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs860487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs866680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs895662	0.88[EUR][1000 genomes]
rs895665	0.92[EUR][1000 genomes];0.93[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs829664	LYCAT	cis	multi-tissue	Pritchard
rs829664	TMEM214	cis	cerebellum	SCAN
rs829664	TMEM214	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30715600-30732800	Weak transcription	Hela-S3	cervix
2	chr2:30716000-30726000	Weak transcription	Aorta	Aorta
3	chr2:30716000-30727600	Weak transcription	Small Intestine	intestine
4	chr2:30716000-30728000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:30716200-30726400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:30716200-30726600	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:30721200-30727400	Weak transcription	NHLF	lung
8	chr2:30721400-30728400	Weak transcription	Liver	Liver
9	chr2:30721400-30739000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:30722000-30727600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:30722200-30725800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:30724000-30725800	Weak transcription	Pancreas	Pancrea
13	chr2:30724000-30726000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:30724000-30726000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:30724000-30726400	Weak transcription	Fetal Heart	heart
16	chr2:30724000-30727400	Weak transcription	NHDF-Ad	bronchial
17	chr2:30724000-30732600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:30724200-30726000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:30724200-30726000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:30724200-30726000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:30724200-30726000	Weak transcription	Fetal Lung	lung
22	chr2:30724200-30726000	Weak transcription	Right Ventricle	heart
23	chr2:30724200-30726200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:30724200-30726400	Weak transcription	A549	lung
25	chr2:30724200-30727200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:30724200-30727600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:30724200-30728000	Weak transcription	HepG2	liver
28	chr2:30724200-30728400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:30724200-30728400	Weak transcription	K562	blood
30	chr2:30724200-30733400	Weak transcription	Fetal Intestine Large	intestine
31	chr2:30724200-30733800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:30724200-30734000	Weak transcription	Ovary	ovary
33	chr2:30724200-30737400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:30724400-30725800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:30724600-30725800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:30724600-30725800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr2:30724600-30726600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:30724600-30737400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:30725000-30726200	Enhancers	Primary T cells from cord blood	blood
40	chr2:30725200-30726200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
41	chr2:30725200-30729000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:30725200-30729000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr2:30725200-30729000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr2:30725400-30725800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr2:30725400-30726200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:30725400-30728200	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr2:30725400-30729000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:30725400-30729000	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr2:30725600-30725800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:30725600-30726200	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links