Variant report

Variant	rs6492722
Chromosome Location	chr13:95262116-95262117
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	chr13:95253721..95257093-chr13:95258270..95263356,4	K562	blood:
2	chr13:95253328..95256713-chr13:95260193..95262168,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152749	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs16949940	0.80[CEU][hapmap]
rs16949977	1.00[ASN][1000 genomes]
rs2146822	1.00[ASN][1000 genomes]
rs2226077	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2226078	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417425	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4516070	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59149020	1.00[ASN][1000 genomes]
rs61707735	1.00[ASN][1000 genomes]
rs61965606	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492724	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72638354	1.00[ASN][1000 genomes]
rs72638356	1.00[ASN][1000 genomes]
rs7318105	1.00[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320230	1.00[ASN][1000 genomes]
rs7329965	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329985	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73546690	1.00[ASN][1000 genomes]
rs7981150	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984105	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7989918	1.00[ASN][1000 genomes]
rs7998457	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516431	1.00[ASN][1000 genomes]
rs9516436	0.80[CEU][hapmap];1.00[CHD][hapmap]
rs9516439	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524564	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524575	1.00[ASN][1000 genomes]
rs9524577	1.00[ASN][1000 genomes]
rs9584241	1.00[ASN][1000 genomes]
rs9584242	1.00[ASN][1000 genomes]
rs9584243	1.00[ASN][1000 genomes]
rs9590039	0.80[CEU][hapmap];1.00[CHD][hapmap]
rs9590043	0.80[CEU][hapmap]
rs9590045	1.00[ASN][1000 genomes]
rs9590046	1.00[ASN][1000 genomes]
rs9590048	1.00[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6492722	GPR180	cis	Muscle Skeletal	GTEx
rs6492722	GPR180	cis	cerebellum	SCAN
rs6492722	GPR180	cis	parietal	SCAN

Chromatin state (count:120 , 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	chr13:95254800-95263000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr13:95254800-95263800	Weak transcription	Left Ventricle	heart
5	chr13:95254800-95263800	Weak transcription	Pancreas	Pancrea
6	chr13:95254800-95263800	Weak transcription	Psoas Muscle	Psoas
7	chr13:95254800-95268200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr13:95254800-95272000	Weak transcription	Lung	lung
9	chr13:95254800-95275400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr13:95254800-95275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:95255000-95262800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:95255000-95262800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr13:95255000-95263200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr13:95255000-95263200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr13:95255000-95275400	Weak transcription	Aorta	Aorta
17	chr13:95255000-95275600	Weak transcription	Right Ventricle	heart
18	chr13:95255000-95276200	Weak transcription	HSMMtube	muscle
19	chr13:95255000-95281000	Weak transcription	Colonic Mucosa	Colon
20	chr13:95255200-95262800	Weak transcription	Fetal Kidney	kidney
21	chr13:95255200-95272200	Weak transcription	Colon Smooth Muscle	Colon
22	chr13:95255200-95276200	Weak transcription	Fetal Brain Female	brain
23	chr13:95255200-95278200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
25	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr13:95255600-95268000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
28	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
29	chr13:95255800-95263600	Weak transcription	Fetal Intestine Small	intestine
30	chr13:95255800-95264400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr13:95255800-95268000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr13:95255800-95278000	Weak transcription	Hela-S3	cervix
33	chr13:95255800-95284000	Weak transcription	K562	blood
34	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr13:95256400-95262800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr13:95256600-95272000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr13:95257000-95262800	Weak transcription	Thymus	Thymus
38	chr13:95257000-95263800	Weak transcription	Esophagus	oesophagus
39	chr13:95257400-95263200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr13:95257400-95264200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr13:95257400-95267600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr13:95257400-95267800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr13:95257400-95268600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:95257400-95269000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr13:95257600-95267600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr13:95257600-95267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr13:95257600-95268600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr13:95257600-95268600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr13:95258000-95267200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr13:95258000-95267600	Strong transcription	Monocytes-CD14+_RO01746	blood

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