Variant report

Variant	rs13421972
Chromosome Location	chr2:11740177-11740178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11737451..11740720-chr2:11742097..11745716,3	MCF-7	breast:
2	chr2:11739453..11742441-chr2:11747484..11750945,3	MCF-7	breast:
3	chr2:11740125..11742102-chr2:11743265..11746041,3	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LPIN1-4	chr2:11739875-11740900	NONHSAT069180
2	lnc-LPIN1-4	chr2:11739768-11740904	ucscGeneNc_uc002rbr_1
3	lnc-LPIN1-4	chr2:11739768-11740905	NONHSAT069181

No data

Variant related genes	Relation type
ENSG00000265583	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1036393	1.00[ASN][1000 genomes]
rs11538448	1.00[ASN][1000 genomes]
rs11675463	1.00[ASN][1000 genomes]
rs11676175	1.00[ASN][1000 genomes]
rs11677240	1.00[ASN][1000 genomes]
rs11683719	1.00[ASN][1000 genomes]
rs11689869	0.95[EUR][1000 genomes]
rs11890442	1.00[ASN][1000 genomes]
rs11892871	1.00[ASN][1000 genomes]
rs11894146	1.00[ASN][1000 genomes]
rs11894751	1.00[ASN][1000 genomes]
rs1561010	1.00[ASN][1000 genomes]
rs1561011	1.00[ASN][1000 genomes]
rs16857679	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252958	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs34592059	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34928762	1.00[ASN][1000 genomes]
rs3828298	0.89[CEU][hapmap]
rs45509591	1.00[ASN][1000 genomes]
rs55890755	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56788115	1.00[ASN][1000 genomes]
rs57097271	1.00[ASN][1000 genomes]
rs59085046	1.00[ASN][1000 genomes]
rs59408163	1.00[ASN][1000 genomes]
rs60662456	1.00[ASN][1000 genomes]
rs61239977	1.00[ASN][1000 genomes]
rs62113260	1.00[ASN][1000 genomes]
rs62113263	1.00[ASN][1000 genomes]
rs62113264	1.00[ASN][1000 genomes]
rs62113265	1.00[ASN][1000 genomes]
rs62113266	1.00[ASN][1000 genomes]
rs62113267	1.00[ASN][1000 genomes]
rs62113293	1.00[ASN][1000 genomes]
rs62113296	1.00[ASN][1000 genomes]
rs62113297	1.00[ASN][1000 genomes]
rs62113298	1.00[ASN][1000 genomes]
rs62113299	1.00[ASN][1000 genomes]
rs62113300	1.00[ASN][1000 genomes]
rs62113302	1.00[ASN][1000 genomes]
rs62113303	1.00[ASN][1000 genomes]
rs62113305	1.00[ASN][1000 genomes]
rs62113307	1.00[ASN][1000 genomes]
rs62113308	1.00[ASN][1000 genomes]
rs62113309	1.00[ASN][1000 genomes]
rs62113310	1.00[ASN][1000 genomes]
rs62113313	1.00[ASN][1000 genomes]
rs62113354	1.00[ASN][1000 genomes]
rs62113357	1.00[ASN][1000 genomes]
rs62116185	1.00[ASN][1000 genomes]
rs62116208	1.00[ASN][1000 genomes]
rs62116209	1.00[ASN][1000 genomes]
rs6707885	1.00[ASN][1000 genomes]
rs6716999	1.00[ASN][1000 genomes]
rs6717771	1.00[ASN][1000 genomes]
rs6726960	1.00[ASN][1000 genomes]
rs6730352	0.94[EUR][1000 genomes]
rs6744695	1.00[ASN][1000 genomes]
rs6744803	1.00[ASN][1000 genomes]
rs71446421	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72773987	1.00[ASN][1000 genomes]
rs72773997	1.00[ASN][1000 genomes]
rs72773999	1.00[ASN][1000 genomes]
rs72774000	1.00[ASN][1000 genomes]
rs7566112	1.00[ASN][1000 genomes]
rs7569901	1.00[ASN][1000 genomes]
rs7570139	1.00[ASN][1000 genomes]
rs7575000	1.00[ASN][1000 genomes]
rs7593837	1.00[ASN][1000 genomes]
rs7596162	1.00[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13421972	GRHL1	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:11723000-11740400	Weak transcription	Liver	Liver
8	chr2:11724400-11788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:11724600-11741000	Weak transcription	Brain Anterior Caudate	brain
10	chr2:11724600-11766800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:11724600-11766800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:11724800-11749600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:11725000-11743800	Weak transcription	Fetal Kidney	kidney
14	chr2:11725400-11742400	Strong transcription	Ovary	ovary
15	chr2:11725600-11766800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:11733400-11750800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:11733600-11750600	Weak transcription	Pancreas	Pancrea
18	chr2:11733600-11784000	Strong transcription	HepG2	liver
19	chr2:11735200-11744600	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr2:11735200-11746400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:11735600-11745000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:11735600-11746600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:11736000-11743000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:11736200-11741000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:11736200-11765000	Weak transcription	Fetal Lung	lung
26	chr2:11736400-11755400	Weak transcription	Brain Substantia Nigra	brain
27	chr2:11736600-11741000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:11736600-11750600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:11736800-11762800	Weak transcription	Fetal Heart	heart
30	chr2:11737000-11744600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:11737400-11741600	Strong transcription	Brain Hippocampus Middle	brain
32	chr2:11737600-11742000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:11737600-11744400	Strong transcription	Fetal Stomach	stomach
34	chr2:11737800-11740200	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr2:11737800-11745000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:11737800-11746400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:11738000-11744600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:11738400-11744000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:11738600-11741400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr2:11738600-11743400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:11738600-11744800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:11738800-11741000	Weak transcription	Brain Angular Gyrus	brain
43	chr2:11739000-11740800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:11739200-11740200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:11739200-11743000	Weak transcription	Left Ventricle	heart
46	chr2:11739200-11751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:11739200-11752000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:11739600-11744800	Strong transcription	Fetal Muscle Leg	muscle
49	chr2:11739600-11750800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:11740000-11742200	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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