Variant report

Variant	rs10201729
Chromosome Location	chr2:30716761-30716762
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	chr2:30716357..30718643-chr2:30723670..30726399,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10180482	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10202174	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10495777	0.81[ASN][1000 genomes]
rs12053230	0.81[ASN][1000 genomes]
rs12993078	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13014119	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017224	0.93[ASN][1000 genomes]
rs13025287	0.82[ASN][1000 genomes]
rs13395754	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1357850	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1525063	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17038632	0.84[ASN][1000 genomes]
rs2076932	0.82[EUR][1000 genomes]
rs28666424	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35116667	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36072623	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56150357	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62139608	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6705814	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6724421	0.93[EUR][1000 genomes]
rs6739322	0.84[ASN][1000 genomes]
rs894788	0.88[EUR][1000 genomes];0.85[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
rs10201729	LYCAT	Cis_1M	lymphoblastoid	RTeQTL
rs10201729	LYCAT	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30697800-30720800	Weak transcription	Thymus	Thymus
2	chr2:30704600-30719600	Weak transcription	Right Atrium	heart
3	chr2:30704600-30719800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:30704600-30720600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:30711400-30717000	Weak transcription	Lung	lung
6	chr2:30711400-30717800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr2:30711400-30720600	Weak transcription	NHDF-Ad	bronchial
8	chr2:30711600-30723600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:30711800-30717400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:30712000-30717400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:30713000-30720600	Weak transcription	Primary T cells from cord blood	blood
12	chr2:30714400-30723600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:30715200-30716800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:30715400-30717200	Enhancers	Primary B cells from cord blood	blood
15	chr2:30715600-30719000	Weak transcription	Dnd41	blood
16	chr2:30715600-30723800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:30715600-30732800	Weak transcription	Hela-S3	cervix
18	chr2:30715800-30719000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr2:30715800-30721400	Weak transcription	Stomach Mucosa	stomach
20	chr2:30716000-30720400	Weak transcription	Fetal Kidney	kidney
21	chr2:30716000-30720800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:30716000-30723800	Weak transcription	Ovary	ovary
23	chr2:30716000-30726000	Weak transcription	Aorta	Aorta
24	chr2:30716000-30727600	Weak transcription	Small Intestine	intestine
25	chr2:30716000-30728000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:30716200-30719200	Weak transcription	A549	lung
27	chr2:30716200-30720600	Weak transcription	HSMM	muscle
28	chr2:30716200-30720600	Weak transcription	NHLF	lung
29	chr2:30716200-30726400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:30716200-30726600	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:30716400-30717200	Enhancers	Psoas Muscle	Psoas
32	chr2:30716400-30720000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:30716600-30717000	Weak transcription	Fetal Heart	heart
34	chr2:30716600-30717200	Enhancers	Left Ventricle	heart
35	chr2:30716600-30719400	Weak transcription	Fetal Lung	lung
36	chr2:30716600-30720800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:30716600-30723800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links