Variant report

Variant	rs401072
Chromosome Location	chr15:93211991-93211992
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	chr15:93207992..93209553-chr15:93211342..93213959,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11857315	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12907094	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910861	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1467972	0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs172263	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs172264	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs285722	0.80[YRI][hapmap]
rs285733	1.00[JPT][hapmap]
rs285746	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs285747	0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs285753	0.91[MEX][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap]
rs374653	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs376138	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs380184	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs389334	0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs391059	0.96[EUR][1000 genomes]
rs413646	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs438230	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs99521	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1036897	chr15:93211991-93239388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs401072	IQGAP1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93207200-93213000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:93208200-93212000	Enhancers	Fetal Intestine Small	intestine
3	chr15:93208400-93212000	Enhancers	Fetal Kidney	kidney
4	chr15:93209400-93212000	Enhancers	Ovary	ovary
5	chr15:93210000-93212000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:93210800-93212000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:93210800-93212000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr15:93210800-93212800	Weak transcription	HSMMtube	muscle
9	chr15:93211000-93212000	Enhancers	HepG2	liver
10	chr15:93211200-93212000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr15:93211200-93212200	Enhancers	Fetal Lung	lung
12	chr15:93211200-93212600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:93211200-93212800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:93211200-93212800	Weak transcription	HSMM	muscle
15	chr15:93211200-93214800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:93211200-93218000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:93211400-93212000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr15:93211600-93212000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr15:93211600-93212000	Enhancers	A549	lung
20	chr15:93211600-93213000	Weak transcription	Fetal Intestine Large	intestine
21	chr15:93211600-93213200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr15:93211600-93214000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:93211600-93214600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:93211600-93221400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:93211800-93212000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
26	chr15:93211800-93212800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:93211800-93213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:93211800-93216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:93211800-93216600	Weak transcription	Fetal Stomach	stomach
30	chr15:93211800-93218400	Weak transcription	Right Atrium	heart
31	chr15:93211800-93224400	Weak transcription	Fetal Muscle Leg	muscle

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