Variant report

Variant	rs7129995
Chromosome Location	chr11:18335390-18335391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10734259	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741741	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741742	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832917	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10832921	0.91[EUR][1000 genomes]
rs11024634	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1140047	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286683	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12293544	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1520884	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061163	0.82[AMR][1000 genomes]
rs2061164	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124374	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740711	0.91[EUR][1000 genomes]
rs3802968	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825025	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150526	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150550	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150561	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150562	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150564	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150566	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150575	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150579	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150588	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150609	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4150610	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150612	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150615	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150616	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150622	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150641	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4150642	1.00[ASN][1000 genomes]
rs4150650	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4150651	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4150653	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150655	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4150661	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4150673	0.91[EUR][1000 genomes]
rs4353250	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486419	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7103375	0.87[ASN][1000 genomes]
rs7947378	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9783347	0.90[EUR][1000 genomes]
rs9988866	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7129995	GTF2H1	cis	Esophagus Mucosa	GTEx
rs7129995	GTF2H1	cis	Esophagus Muscularis	GTEx
rs7129995	GTF2H1	cis	Stomach	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18300200-18336000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr11:18311800-18343000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:18317200-18342200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:18320600-18337400	Weak transcription	Gastric	stomach
5	chr11:18327800-18342200	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:18327800-18342200	Weak transcription	HUVEC	blood vessel
7	chr11:18330200-18340000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:18330200-18340800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr11:18331000-18341000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:18331000-18341600	Weak transcription	Fetal Lung	lung
11	chr11:18331000-18342200	Weak transcription	Right Ventricle	heart
12	chr11:18331600-18341600	Weak transcription	Psoas Muscle	Psoas
13	chr11:18331800-18335600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:18331800-18335600	Weak transcription	Aorta	Aorta
15	chr11:18331800-18336600	Weak transcription	Spleen	Spleen
16	chr11:18332000-18341800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:18332200-18335800	Enhancers	HMEC	breast
18	chr11:18332200-18336400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:18332200-18342200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:18332400-18335400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr11:18332400-18336200	Weak transcription	Left Ventricle	heart
22	chr11:18332600-18335800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:18332600-18337400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:18332600-18340000	Weak transcription	Liver	Liver
25	chr11:18332600-18341000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:18332600-18342800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:18332600-18342800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr11:18332600-18343000	Weak transcription	Lung	lung
29	chr11:18332800-18337400	Weak transcription	Fetal Brain Female	brain
30	chr11:18332800-18340800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr11:18332800-18341000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr11:18332800-18341800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr11:18332800-18341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:18332800-18342200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:18332800-18342200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:18332800-18342800	Weak transcription	Fetal Brain Male	brain
37	chr11:18333000-18335600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:18333000-18336000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr11:18333000-18336600	Enhancers	HSMMtube	muscle
40	chr11:18333000-18338200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:18333000-18341600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr11:18333000-18341800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr11:18333000-18341800	Weak transcription	Thymus	Thymus
44	chr11:18333000-18342000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:18333000-18342000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr11:18333000-18342000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr11:18333000-18342200	Weak transcription	Adipose Nuclei	Adipose
48	chr11:18333000-18342400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr11:18333000-18342400	Weak transcription	Colonic Mucosa	Colon
50	chr11:18333000-18342800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links