Variant report

Variant	rs7981788
Chromosome Location	chr13:95263924-95263925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95246300..95249639-chr13:95263830..95266634,3	MCF-7	breast:
2	chr13:95258888..95260648-chr13:95263620..95266096,2	K562	blood:

Variant related genes	Relation type
ENSG00000088451	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1112370	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1341267	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1408999	0.81[EUR][1000 genomes]
rs1572935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2275648	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2298055	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2298056	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2298057	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34350725	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34405130	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35253817	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742107	0.81[CEU][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3897473	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3897474	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4238308	0.98[ASN][1000 genomes]
rs4296139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4465476	0.92[ASN][1000 genomes]
rs4473052	0.81[EUR][1000 genomes]
rs4608209	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4771890	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4773801	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6492716	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6492718	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6492720	0.97[ASN][1000 genomes]
rs6492721	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6492723	0.98[ASN][1000 genomes]
rs6492725	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7321239	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7326576	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7330873	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7331814	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7339106	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7997035	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7997333	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7998025	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9301979	0.81[CEU][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9301981	0.85[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9301983	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9516437	0.85[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9516438	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9516440	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9516441	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9516443	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9516445	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9524544	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524545	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524547	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9524548	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524549	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524550	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524551	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9524553	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9524554	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9524555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524556	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524559	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524560	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9524561	0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9524562	0.80[JPT][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9524563	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9524566	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs9524568	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9556402	0.80[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9556405	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561642	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9561643	0.90[ASN][1000 genomes]
rs9561645	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9590037	0.88[AMR][1000 genomes];0.89[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	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7981788	GPR180	cis	lung	GTEx
rs7981788	GPR180	cis	Muscle Skeletal	GTEx
rs7981788	GPR180	cis	Esophagus Mucosa	GTEx
rs7981788	GPR180	cis	Artery Tibial	GTEx
rs7981788	GPR180	cis	Adipose Subcutaneous	GTEx
rs7981788	GPR180	cis	Nerve Tibial	GTEx
rs7981788	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs7981788	GPR180	cis	Stomach	GTEx
rs7981788	GPR180	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254600-95276600	Weak transcription	Small Intestine	intestine
2	chr13:95254600-95284000	Weak transcription	Spleen	Spleen
3	chr13:95254800-95268200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr13:95254800-95272000	Weak transcription	Lung	lung
5	chr13:95254800-95275400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr13:95254800-95275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:95255000-95275400	Weak transcription	Aorta	Aorta
9	chr13:95255000-95275600	Weak transcription	Right Ventricle	heart
10	chr13:95255000-95276200	Weak transcription	HSMMtube	muscle
11	chr13:95255000-95281000	Weak transcription	Colonic Mucosa	Colon
12	chr13:95255200-95272200	Weak transcription	Colon Smooth Muscle	Colon
13	chr13:95255200-95276200	Weak transcription	Fetal Brain Female	brain
14	chr13:95255200-95278200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
16	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr13:95255600-95268000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
19	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
20	chr13:95255800-95264400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr13:95255800-95268000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr13:95255800-95278000	Weak transcription	Hela-S3	cervix
23	chr13:95255800-95284000	Weak transcription	K562	blood
24	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr13:95256600-95272000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr13:95257400-95264200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr13:95257400-95267600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr13:95257400-95267800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr13:95257400-95268600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:95257400-95269000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:95257600-95267600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr13:95257600-95267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr13:95257600-95268600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr13:95257600-95268600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:95258000-95267200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr13:95258000-95267600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr13:95259000-95275400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr13:95259600-95275400	Weak transcription	Primary B cells from cord blood	blood
39	chr13:95259600-95275400	Weak transcription	Brain Hippocampus Middle	brain
40	chr13:95259800-95264000	Weak transcription	Ovary	ovary
41	chr13:95259800-95265200	Weak transcription	NHEK	skin
42	chr13:95259800-95266200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr13:95259800-95268600	Strong transcription	Dnd41	blood
44	chr13:95259800-95269000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr13:95259800-95275800	Weak transcription	Gastric	stomach
46	chr13:95259800-95276000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr13:95259800-95282000	Weak transcription	Brain Germinal Matrix	brain
48	chr13:95260000-95264000	Weak transcription	Fetal Stomach	stomach
49	chr13:95260000-95265800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr13:95260000-95270400	Weak transcription	HMEC	breast

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