Variant report

Variant	rs2353354
Chromosome Location	chr7:138266009-138266010
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:138260494..138262791-chr7:138264344..138267243,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10155993	0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10215281	0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10227693	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10232771	0.83[ASN][1000 genomes]
rs10246196	0.84[JPT][hapmap]
rs10247380	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10248731	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10258706	0.82[ASN][1000 genomes]
rs1030961	0.85[ASN][1000 genomes]
rs1077772	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs1116324	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11976614	0.80[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs12112459	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12666310	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371463	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1421604	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1544733	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1614641	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1616318	0.83[ASN][1000 genomes]
rs1659830	0.89[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs1659831	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1659832	0.89[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1673203	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1673204	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673205	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1673206	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1673207	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1673211	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17364560	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17461551	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1813003	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1874326	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs2029814	0.84[JPT][hapmap]
rs2029815	0.84[JPT][hapmap]
rs2353351	0.84[JPT][hapmap]
rs2353355	0.96[ASN][1000 genomes]
rs3757381	0.85[ASN][1000 genomes]
rs3778705	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3807155	0.80[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs3807156	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3807157	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55723768	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56092804	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57407834	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58562866	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62485261	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62485263	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62485264	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62487615	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62487616	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62487619	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6467776	0.80[ASN][1000 genomes]
rs6467778	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6467780	0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs6467782	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6467783	0.91[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs6948094	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs6954285	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6959574	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6963539	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6970175	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6974877	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6978524	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs728092	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs749546	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7795981	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs888609	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9791462	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9791634	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs985299	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[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	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2353354	LUC7L2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138242600-138272400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
2	chr7:138250200-138273800	Weak transcription	Gastric	stomach
3	chr7:138250400-138267600	Weak transcription	NHLF	lung
4	chr7:138250400-138272000	Weak transcription	Small Intestine	intestine
5	chr7:138250400-138273000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:138250600-138270600	Weak transcription	Fetal Brain Male	brain
7	chr7:138250600-138271800	Weak transcription	Right Ventricle	heart
8	chr7:138250600-138273000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:138250600-138273400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:138250800-138272400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:138250800-138272600	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr7:138250800-138273200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:138251000-138267800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:138251000-138272800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:138251000-138272800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:138251200-138272800	Strong transcription	Fetal Thymus	thymus
17	chr7:138251200-138273000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:138251400-138266200	Strong transcription	Primary B cells from cord blood	blood
19	chr7:138251400-138270800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:138251400-138273000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr7:138251400-138273000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:138251600-138273200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:138252000-138266600	Strong transcription	Primary T cells from cord blood	blood
24	chr7:138252000-138270800	Strong transcription	HepG2	liver
25	chr7:138252000-138272800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr7:138252200-138270400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:138252200-138271800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:138252200-138272200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr7:138252200-138273000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr7:138252400-138272600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:138252400-138272800	Strong transcription	Liver	Liver
32	chr7:138252400-138273000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:138252600-138270400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr7:138252600-138272200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:138252600-138272800	Strong transcription	Dnd41	blood
36	chr7:138253000-138272400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:138253200-138270200	Strong transcription	Fetal Intestine Large	intestine
38	chr7:138253400-138268400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr7:138253600-138270800	Strong transcription	K562	blood
40	chr7:138254200-138273000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:138254600-138272000	Weak transcription	HMEC	breast
42	chr7:138256200-138267600	Weak transcription	Esophagus	oesophagus
43	chr7:138256200-138267600	Weak transcription	Spleen	Spleen
44	chr7:138256200-138273600	Weak transcription	Brain Substantia Nigra	brain
45	chr7:138256400-138267800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:138256400-138269800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:138256400-138272200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr7:138256400-138273600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:138256400-138273600	Weak transcription	NHEK	skin
50	chr7:138256400-138274000	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links