Variant report

Variant	rs11935024
Chromosome Location	chr4:100944275-100944276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:100932443..100934795-chr4:100942614..100944305,2	K562	blood:
2	chr4:100933295..100935388-chr4:100941563..100944305,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10026048	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097676	0.95[JPT][hapmap]
rs11097677	0.95[JPT][hapmap]
rs11732776	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11935399	0.85[ASN][1000 genomes]
rs1365491	0.95[JPT][hapmap]
rs1365492	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[ASN][1000 genomes]
rs17029563	0.95[JPT][hapmap]
rs1896166	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961323	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2070738	0.88[ASW][hapmap];0.88[CEU][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap]
rs2098937	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2114442	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2298735	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28404345	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2866174	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2866180	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706589	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3756087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775501	0.95[JPT][hapmap]
rs3775511	0.89[ASN][1000 genomes]
rs60978748	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6532833	0.95[JPT][hapmap]
rs6532835	0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6532836	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6811559	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824513	0.81[AFR][1000 genomes]
rs6831193	0.82[AFR][1000 genomes]
rs6838495	0.83[AFR][1000 genomes]
rs6842840	0.88[ASW][hapmap];0.81[LWK][hapmap]
rs6848337	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6849599	0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6854536	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7660185	0.81[AFR][1000 genomes]
rs7675947	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7676564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7684872	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7686428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7689566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7692416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919132	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs919133	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs9307242	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1000173	chr4:100928002-100964404	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv427689	chr4:100931741-101216531	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11935024	MAPKSP1	cis	parietal	SCAN
rs11935024	MAPKSP1	cis	cerebellum	SCAN
rs11935024	NFKB1	cis	cerebellum	SCAN
rs11935024	NHEDC1	cis	cerebellum	SCAN
rs11935024	DAPP1	Cis_1M	lymphoblastoid	RTeQTL
rs11935024	NHEDC2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100943000-100946000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr4:100943200-100945400	Enhancers	Fetal Heart	heart
3	chr4:100943400-100944600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:100943400-100944600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:100943600-100944600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr4:100943800-100944400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:100943800-100944400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:100943800-100944600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr4:100943800-100944600	Enhancers	Colon Smooth Muscle	Colon
10	chr4:100943800-100944800	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr4:100944000-100944400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr4:100944000-100944600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:100944000-100944600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr4:100944000-100944600	Enhancers	Brain Germinal Matrix	brain
15	chr4:100944000-100944600	Enhancers	Fetal Stomach	stomach
16	chr4:100944000-100945800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:100944200-100944400	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links