Variant report

Variant	rs8002042
Chromosome Location	chr13:80060687-80060688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:80053858..80056756-chr13:80060556..80063243,3	MCF-7	breast:
2	chr13:80060446..80062114-chr13:80062702..80064410,2	K562	blood:

Variant related genes	Relation type
ENSG00000102471	Chromatin interaction
ENSG00000232132	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs1208049	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1212082	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12865187	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12871015	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12877507	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1324868	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1335368	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1335370	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1408049	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1408658	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1409018	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1410336	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1414155	0.89[ASN][1000 genomes]
rs1414156	0.89[ASN][1000 genomes]
rs1475797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1577416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1577418	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1748761	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs1748768	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1752648	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1752649	0.82[JPT][hapmap]
rs1853830	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2025913	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2057573	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2065743	0.91[ASN][1000 genomes]
rs2182009	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2182010	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2182873	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2265377	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs2265378	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2274555	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2476172	0.81[ASN][1000 genomes]
rs2476173	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484343	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484344	0.81[ASN][1000 genomes]
rs2484345	0.88[AMR][1000 genomes]
rs2760101	0.90[ASN][1000 genomes]
rs2760102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2760103	0.88[ASN][1000 genomes]
rs2760105	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760106	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2763809	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs2763810	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2783119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783120	0.92[ASN][1000 genomes]
rs2783121	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2783122	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2783125	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2783126	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2876740	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs314687	0.84[ASN][1000 genomes]
rs314688	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs314690	0.85[AFR][1000 genomes]
rs3187338	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3742117	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs3742118	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs3742119	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3742122	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3752994	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3818563	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs386603	0.85[ASN][1000 genomes]
rs3903388	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs4145207	0.96[ASN][1000 genomes]
rs4146473	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs4476060	0.87[ASN][1000 genomes]
rs4885633	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4885634	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885636	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs643778	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs6563098	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6563100	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6563104	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6563110	0.81[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563115	0.92[ASN][1000 genomes]
rs6563116	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs700396	0.88[ASN][1000 genomes]
rs7317343	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7317416	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7319252	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs7319320	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7321953	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7322167	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7322673	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs73235963	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7325095	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7327386	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs7327603	0.82[JPT][hapmap]
rs7328494	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs7329331	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7331872	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7332367	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7332913	0.82[JPT][hapmap]
rs7336581	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7338530	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7339303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7981067	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7982263	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7987193	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs7987769	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7988601	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7988784	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7990344	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7996493	0.94[ASN][1000 genomes]
rs7996652	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7998837	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs8001281	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs912639	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs9318621	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9318623	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9318625	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9318626	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9318627	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9318634	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9318640	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs9318641	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs9318644	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9530899	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs9530901	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9530913	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9530914	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9530922	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9530925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9545065	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9545066	0.81[CHB][hapmap]
rs9545067	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9545076	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9545083	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9545085	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs9545086	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs9545087	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9545097	0.89[CEU][hapmap];0.87[JPT][hapmap]
rs9545101	0.81[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs9545142	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9565486	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9565489	0.82[JPT][hapmap]
rs9565497	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs9565510	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9574409	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9574416	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9574418	0.81[AMR][1000 genomes]
rs9574422	0.89[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs9574429	0.87[ASN][1000 genomes]
rs9574434	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9593396	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs9593399	0.87[ASN][1000 genomes]
rs9601240	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9601242	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs987284	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

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	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8002042	RP11-25J23.3	cis	Thyroid	GTEx
rs8002042	RP11-25J23.3	cis	lung	GTEx
rs8002042	RBM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80056200-80060800	Weak transcription	Gastric	stomach
2	chr13:80056200-80063200	Weak transcription	Left Ventricle	heart
3	chr13:80056200-80066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:80056200-80066600	Weak transcription	Psoas Muscle	Psoas
5	chr13:80056200-80077400	Weak transcription	Right Ventricle	heart
6	chr13:80056600-80064200	Weak transcription	Placenta	Placenta
7	chr13:80056800-80061200	Enhancers	Fetal Heart	heart
8	chr13:80056800-80064000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr13:80056800-80064400	Weak transcription	Fetal Stomach	stomach
10	chr13:80056800-80065800	Weak transcription	Fetal Muscle Leg	muscle
11	chr13:80057000-80063600	Weak transcription	Right Atrium	heart
12	chr13:80057000-80066200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:80057400-80060800	Enhancers	HSMM	muscle
14	chr13:80057400-80063400	Weak transcription	GM12878-XiMat	blood
15	chr13:80057400-80064600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr13:80057600-80061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:80057600-80065400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr13:80057600-80065600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:80057800-80064600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr13:80057800-80064600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr13:80058000-80065400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr13:80058400-80061400	Enhancers	Stomach Mucosa	stomach
23	chr13:80058400-80062600	Enhancers	Fetal Intestine Small	intestine
24	chr13:80058600-80061200	Enhancers	NHDF-Ad	bronchial
25	chr13:80058600-80065800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr13:80059000-80077200	Weak transcription	Small Intestine	intestine
27	chr13:80059400-80061600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr13:80059400-80062200	Enhancers	Liver	Liver
29	chr13:80059400-80064800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr13:80059400-80066400	Weak transcription	Fetal Thymus	thymus
31	chr13:80059600-80060800	Enhancers	HepG2	liver
32	chr13:80059600-80061000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr13:80059600-80061600	Enhancers	Fetal Intestine Large	intestine
34	chr13:80059600-80063200	Weak transcription	Brain Hippocampus Middle	brain
35	chr13:80059600-80063200	Weak transcription	Pancreas	Pancrea
36	chr13:80059600-80064200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:80059600-80064200	Weak transcription	Esophagus	oesophagus
38	chr13:80059600-80064200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr13:80059600-80064600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr13:80059600-80064600	Weak transcription	Colon Smooth Muscle	Colon
41	chr13:80059600-80066200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:80059600-80066600	Weak transcription	Brain Angular Gyrus	brain
43	chr13:80059600-80068800	Weak transcription	Brain Substantia Nigra	brain
44	chr13:80059800-80060800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr13:80059800-80060800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr13:80059800-80061000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr13:80059800-80061000	Weak transcription	Fetal Kidney	kidney
48	chr13:80059800-80062200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr13:80059800-80062600	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr13:80059800-80063000	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links