Variant report

Variant	rs9516438
Chromosome Location	chr13:95249017-95249018
allele	C/T
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	TAF1	chr13:95247908-95249042	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr13:95247191-95249090	HepG2	liver:	n/a	n/a
3	E2F6	chr13:95248206-95249086	H1-hESC	embryonic stem cell:	n/a	chr13:95248584-95248593
4	POLR2A	chr13:95247105-95249150	Raji	blood:	n/a	n/a
5	POLR2A	chr13:95247884-95249110	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr13:95247422-95249074	NB4	blood:	n/a	n/a
7	POLR2A	chr13:95247367-95249052	H1-hESC	embryonic stem cell:	n/a	n/a
8	ELF1	chr13:95247883-95249057	GM12878	blood:	n/a	chr13:95248667-95248678
9	POLR2A	chr13:95246537-95249031	GM12891	blood:	n/a	n/a
10	POLR2A	chr13:95247826-95249034	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:95247274..95249727-chr13:95251841..95255221,4	MCF-7	breast:
2	chr13:95246267..95250128-chr13:95251933..95256020,6	MCF-7	breast:
3	chr13:95245952..95249992-chr13:95252491..95255739,5	K562	blood:

Variant related genes	Relation type
TGDS	TF binding region
ENSG00000152749	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1112370	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1408999	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275647	0.95[ASN][1000 genomes]
rs2275648	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298058	0.96[ASN][1000 genomes]
rs34350725	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34405130	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35253817	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35678857	0.94[ASN][1000 genomes]
rs3742107	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3897473	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3897474	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4473052	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4489873	0.95[ASN][1000 genomes]
rs4608209	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4773801	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6492716	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6492717	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6492718	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7321239	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7330873	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7331814	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7339106	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7981788	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7991607	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7997035	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997333	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7998025	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9301979	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9301981	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301983	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516434	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9516437	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516440	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516441	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9516443	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516445	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524544	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524545	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524547	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524548	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524549	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524550	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524551	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524553	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524554	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524555	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524556	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524557	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524559	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9556402	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9556403	0.95[ASN][1000 genomes]
rs9556405	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9561638	0.95[ASN][1000 genomes]
rs9561642	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590037	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3521585	chr13:95244823-95249508	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
5	esv3497281	chr13:95244835-95249503	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
6	esv3497282	chr13:95244837-95249504	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
7	esv3521596	chr13:95244837-95249504	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9516438	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs9516438	GPR180	cis	Esophagus Mucosa	GTEx
rs9516438	GPR180	cis	Artery Tibial	GTEx
rs9516438	GPR180	cis	Muscle Skeletal	GTEx
rs9516438	GPR180	cis	Stomach	GTEx
rs9516438	GPR180	cis	Adipose Subcutaneous	GTEx
rs9516438	GPR180	cis	Nerve Tibial	GTEx
rs9516438	GPR180	cis	Whole Blood	GTEx
rs9516438	GPR180	cis	lung	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95247400-95249200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr13:95247600-95249200	Active TSS	Colonic Mucosa	Colon
3	chr13:95247600-95249200	Active TSS	NHEK	skin
4	chr13:95247800-95249200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr13:95247800-95249200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr13:95247800-95249200	Active TSS	Placenta	Placenta
7	chr13:95247800-95249200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr13:95248000-95249200	Active TSS	Duodenum Mucosa	Duodenum
9	chr13:95248400-95249200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr13:95248600-95249200	Flanking Active TSS	Dnd41	blood
11	chr13:95248800-95249200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:95248800-95253200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:95248800-95253200	Weak transcription	Primary T cells from cord blood	blood
14	chr13:95248800-95253600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr13:95248800-95253600	Weak transcription	HUVEC	blood vessel
16	chr13:95249000-95249200	Enhancers	Primary B cells from peripheral blood	blood
17	chr13:95249000-95249200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr13:95249000-95249200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr13:95249000-95249200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr13:95249000-95249200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr13:95249000-95249200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr13:95249000-95249200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:95249000-95249200	Enhancers	Liver	Liver
24	chr13:95249000-95249200	Enhancers	Fetal Muscle Leg	muscle
25	chr13:95249000-95249200	Enhancers	Fetal Thymus	thymus
26	chr13:95249000-95249200	Enhancers	Pancreas	Pancrea
27	chr13:95249000-95249200	Enhancers	HepG2	liver
28	chr13:95249000-95249200	Enhancers	HMEC	breast
29	chr13:95249000-95250200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr13:95249000-95250200	Weak transcription	NHLF	lung
31	chr13:95249000-95252000	Weak transcription	Fetal Intestine Large	intestine
32	chr13:95249000-95252000	Weak transcription	Stomach Mucosa	stomach
33	chr13:95249000-95252200	Weak transcription	Fetal Intestine Small	intestine
34	chr13:95249000-95252800	Weak transcription	GM12878-XiMat	blood
35	chr13:95249000-95253000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr13:95249000-95253200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:95249000-95253200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:95249000-95253200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr13:95249000-95253200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr13:95249000-95253200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr13:95249000-95253200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr13:95249000-95253200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr13:95249000-95253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr13:95249000-95253200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr13:95249000-95253200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr13:95249000-95253200	Weak transcription	Brain Anterior Caudate	brain
47	chr13:95249000-95253200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr13:95249000-95253200	Weak transcription	Brain Substantia Nigra	brain
49	chr13:95249000-95253200	Weak transcription	Colon Smooth Muscle	Colon
50	chr13:95249000-95253200	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links