Variant report

Variant	rs7130929
Chromosome Location	chr11:18068163-18068164
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr11:18067726-18068253	MCF10A-Er-Src	breast:	n/a	chr11:18067732-18067739
2	GATA3	chr11:18068100-18068285	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
TPH1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10444225	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766452	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766453	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1079785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024462	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024474	0.96[CEU][hapmap]
rs11024478	0.87[CEU][hapmap]
rs12360537	0.91[CEU][hapmap];0.84[TSI][hapmap]
rs12361971	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1399025	0.88[CEU][hapmap]
rs2085275	0.92[CEU][hapmap]
rs3741199	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs4537731	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756930	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs4757610	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757611	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6486403	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7106970	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7110238	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119063	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs7122118	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933593	0.81[ASN][1000 genomes]
rs7936469	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7937368	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7939791	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7943526	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7944348	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7950282	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7950705	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950928	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7951771	0.85[ASN][1000 genomes]
rs871699	0.95[CEU][hapmap]
rs907922	0.96[CEU][hapmap]
rs964834	0.92[CEU][hapmap];0.85[TSI][hapmap]

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	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	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7130929	SERGEF	Cis_1M	lymphoblastoid	RTeQTL
rs7130929	TPH1	cis	cerebellum	SCAN
rs7130929	RPS13	cis	parietal	SCAN
rs7130929	LOC494141	cis	parietal	SCAN
rs7130929	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs7130929	SAAL1	cis	Artery Tibial	GTEx
rs7130929	SAAL1	cis	cerebellum	SCAN
rs7130929	SAAL1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18066400-18069000	Active TSS	Aorta	Aorta
2	chr11:18067400-18068200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr11:18067400-18068200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
4	chr11:18067400-18068200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr11:18067400-18068200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr11:18067400-18068200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr11:18067400-18068200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:18067400-18068200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr11:18067600-18068200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr11:18067600-18068200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:18067600-18068200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:18067600-18068200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
13	chr11:18067600-18068200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:18067600-18068200	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr11:18067600-18068200	Flanking Active TSS	Ovary	ovary
16	chr11:18067600-18068200	Enhancers	Pancreas	Pancrea
17	chr11:18067600-18068200	Active TSS	Right Atrium	heart
18	chr11:18067600-18068200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
19	chr11:18067600-18068400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:18067600-18068400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
21	chr11:18067800-18068200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:18067800-18068200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:18067800-18068200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
24	chr11:18067800-18068200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
25	chr11:18067800-18068200	Bivalent Enhancer	Left Ventricle	heart
26	chr11:18067800-18068200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
27	chr11:18067800-18068200	Bivalent/Poised TSS	NHEK	skin
28	chr11:18067800-18068400	Bivalent Enhancer	Stomach Mucosa	stomach
29	chr11:18068000-18068200	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:18068000-18068200	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
31	chr11:18068000-18068200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
32	chr11:18068000-18068200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
33	chr11:18068000-18068200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:18068000-18068200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:18068000-18068200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:18068000-18068200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr11:18068000-18068200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:18068000-18068200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:18068000-18068200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:18068000-18068200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:18068000-18068200	Bivalent Enhancer	Brain Angular Gyrus	brain
42	chr11:18068000-18068200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
43	chr11:18068000-18068200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
44	chr11:18068000-18068200	Bivalent Enhancer	Esophagus	oesophagus
45	chr11:18068000-18068200	Flanking Bivalent TSS/Enh	Fetal Heart	heart
46	chr11:18068000-18068200	Bivalent Enhancer	Fetal Intestine Small	intestine
47	chr11:18068000-18068200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr11:18068000-18068200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
49	chr11:18068000-18068200	Bivalent Enhancer	Fetal Stomach	stomach
50	chr11:18068000-18068200	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas

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