Variant report

Variant	rs3903388
Chromosome Location	chr13:79904821-79904822
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	chr13:79904552..79907167-chr7:5465284..5467167,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272953	Chromatin interaction

Extended variants
information (count: 215 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:213)

rs_ID	r²[population]
rs1007569	0.97[ASN][1000 genomes]
rs1022891	0.88[JPT][hapmap]
rs1028770	0.94[ASN][1000 genomes]
rs10444623	0.91[ASN][1000 genomes]
rs12865187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12871015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12872328	0.87[ASN][1000 genomes]
rs12875039	0.99[ASN][1000 genomes]
rs12877507	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1324868	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1324870	0.94[ASN][1000 genomes]
rs1335368	0.82[JPT][hapmap]
rs1335370	0.82[JPT][hapmap]
rs1408657	0.99[ASN][1000 genomes]
rs1408658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1409018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1409019	0.97[ASN][1000 genomes]
rs1410332	0.97[ASN][1000 genomes]
rs1410336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1475797	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1577416	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1577418	0.82[JPT][hapmap]
rs1626333	0.94[ASN][1000 genomes]
rs17071512	1.00[YRI][hapmap]
rs17071545	1.00[YRI][hapmap]
rs1748761	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1748767	0.88[ASN][1000 genomes]
rs1748768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1749983	0.97[ASN][1000 genomes]
rs1752646	0.99[ASN][1000 genomes]
rs1752647	0.99[ASN][1000 genomes]
rs1752648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1752649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1853830	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1856996	0.93[ASN][1000 genomes]
rs1856997	0.94[ASN][1000 genomes]
rs1927506	0.97[ASN][1000 genomes]
rs1980883	0.96[ASN][1000 genomes]
rs2025913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2057573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2147566	0.95[ASN][1000 genomes]
rs2182009	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2182010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2182873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2265377	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2265378	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2274555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2760106	0.82[JPT][hapmap]
rs2763809	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2763810	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2765079	0.99[ASN][1000 genomes]
rs2769552	0.95[ASN][1000 genomes]
rs2783119	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs2783121	0.82[JPT][hapmap]
rs2783122	0.82[JPT][hapmap]
rs28579970	0.96[ASN][1000 genomes]
rs2876739	0.95[ASN][1000 genomes]
rs2876740	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3187338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs36152718	0.91[ASN][1000 genomes]
rs3742117	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3742118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3742119	0.96[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]
rs3742122	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3752994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3818563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4146473	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4264284	0.91[ASN][1000 genomes]
rs4328330	0.97[ASN][1000 genomes]
rs4351945	0.92[ASN][1000 genomes]
rs4497554	0.97[ASN][1000 genomes]
rs4573813	0.94[ASN][1000 genomes]
rs4884129	0.97[ASN][1000 genomes]
rs4885625	0.94[ASN][1000 genomes]
rs4885626	0.97[ASN][1000 genomes]
rs4885627	0.97[ASN][1000 genomes]
rs4885628	0.95[ASN][1000 genomes]
rs4885629	0.96[ASN][1000 genomes]
rs4885634	0.82[CEU][hapmap]
rs4885636	0.82[JPT][hapmap]
rs56911077	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs643778	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6563096	0.94[ASN][1000 genomes]
rs6563098	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6563100	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6563104	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6563110	0.80[CEU][hapmap]
rs6563113	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7140027	0.91[ASN][1000 genomes]
rs7317343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7317416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7319212	0.91[ASN][1000 genomes]
rs7319252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7319320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7322167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7322673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7322744	0.97[ASN][1000 genomes]
rs7322756	0.92[ASN][1000 genomes]
rs7324006	0.92[ASN][1000 genomes]
rs7327386	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7327603	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7328494	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7329331	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7331872	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7332004	0.90[ASN][1000 genomes]
rs7332367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7332913	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7333904	0.92[ASN][1000 genomes]
rs7336581	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7338170	0.94[ASN][1000 genomes]
rs7338530	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs7338677	0.97[ASN][1000 genomes]
rs7339303	0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7358847	0.86[ASN][1000 genomes]
rs7981067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7983344	0.94[ASN][1000 genomes]
rs7987193	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7987769	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7988331	0.95[ASN][1000 genomes]
rs7988784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7995243	0.92[ASN][1000 genomes]
rs7996652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7998837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8001281	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs8002042	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs8002633	0.86[ASN][1000 genomes]
rs8002648	0.86[ASN][1000 genomes]
rs912639	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9285309	0.99[ASN][1000 genomes]
rs9285310	0.98[ASN][1000 genomes]
rs9318621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9318623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9318624	0.98[ASN][1000 genomes]
rs9318625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9318626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9318627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9318633	0.89[ASN][1000 genomes]
rs9318634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9318640	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9318641	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs943709	0.93[ASN][1000 genomes]
rs943710	0.94[ASN][1000 genomes]
rs943711	0.93[ASN][1000 genomes]
rs943712	0.93[ASN][1000 genomes]
rs9530889	0.91[ASN][1000 genomes]
rs9530891	0.94[ASN][1000 genomes]
rs9530893	0.96[ASN][1000 genomes]
rs9530894	0.99[ASN][1000 genomes]
rs9530895	0.99[ASN][1000 genomes]
rs9530896	0.99[ASN][1000 genomes]
rs9530897	0.99[ASN][1000 genomes]
rs9530899	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9530900	0.97[ASN][1000 genomes]
rs9530901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9530902	0.90[ASN][1000 genomes]
rs9530904	0.89[ASN][1000 genomes]
rs9530905	0.89[ASN][1000 genomes]
rs9530906	0.87[ASN][1000 genomes]
rs9530913	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9530914	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9545047	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9545048	0.94[ASN][1000 genomes]
rs9545052	0.95[ASN][1000 genomes]
rs9545053	0.95[ASN][1000 genomes]
rs9545054	0.95[ASN][1000 genomes]
rs9545055	0.95[ASN][1000 genomes]
rs9545061	0.98[ASN][1000 genomes]
rs9545063	0.87[ASN][1000 genomes]
rs9545065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9545066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9545067	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545068	0.99[ASN][1000 genomes]
rs9545069	0.99[ASN][1000 genomes]
rs9545073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9545076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9545078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9545079	0.96[ASN][1000 genomes]
rs9545082	0.92[ASN][1000 genomes]
rs9545083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9545085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9545086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9545087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9545090	0.90[ASN][1000 genomes]
rs9545092	0.88[ASN][1000 genomes]
rs9545093	0.88[ASN][1000 genomes]
rs9545097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9545101	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9565482	0.94[ASN][1000 genomes]
rs9565483	0.94[ASN][1000 genomes]
rs9565485	0.96[ASN][1000 genomes]
rs9565486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9565487	0.99[ASN][1000 genomes]
rs9565488	0.99[ASN][1000 genomes]
rs9565489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9565491	0.95[ASN][1000 genomes]
rs9565492	0.97[ASN][1000 genomes]
rs9565497	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9565510	0.81[JPT][hapmap]
rs9574402	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9574405	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9574406	0.98[ASN][1000 genomes]
rs9574409	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9574410	0.98[ASN][1000 genomes]
rs9574411	0.96[ASN][1000 genomes]
rs9574413	1.00[YRI][hapmap]
rs9574416	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9574422	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs9574434	0.82[JPT][hapmap]
rs9593391	0.98[ASN][1000 genomes]
rs9593396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9601211	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9601217	0.91[ASN][1000 genomes]
rs9635027	0.96[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	nsv900586	chr13:79892722-79968467	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv900587	chr13:79894736-79956691	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3903388	RBM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:79882200-79907400	Weak transcription	Fetal Muscle Leg	muscle
2	chr13:79882200-79907600	Weak transcription	Brain Anterior Caudate	brain
3	chr13:79882200-79909800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:79882400-79905000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr13:79882400-79911200	Weak transcription	Left Ventricle	heart
6	chr13:79882400-79911200	Weak transcription	Ovary	ovary
7	chr13:79882400-79914400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:79882400-79925000	Weak transcription	HSMMtube	muscle
9	chr13:79884000-79905200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:79884400-79909000	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:79886400-79911200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr13:79886600-79950200	Weak transcription	Fetal Brain Male	brain
13	chr13:79887000-79907800	Weak transcription	Colon Smooth Muscle	Colon
14	chr13:79887200-79946600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr13:79887800-79907800	Weak transcription	NHLF	lung
16	chr13:79888000-79942800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:79888200-79947000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr13:79888400-79947000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr13:79889400-79905000	Weak transcription	Fetal Intestine Small	intestine
20	chr13:79889400-79909800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr13:79889600-79907800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr13:79889800-79909800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr13:79889800-79916200	Weak transcription	Fetal Heart	heart
24	chr13:79890400-79905000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr13:79891400-79911200	Weak transcription	Esophagus	oesophagus
26	chr13:79891600-79905000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr13:79891600-79911200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr13:79891600-79946800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:79891600-79947000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr13:79891600-79947000	Strong transcription	Dnd41	blood
31	chr13:79891800-79929200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr13:79891800-79935800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr13:79892400-79905200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr13:79892400-79907600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr13:79892800-79928200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr13:79893200-79906000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr13:79893200-79907800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr13:79893200-79957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr13:79893600-79909400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr13:79894200-79910000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr13:79894200-79940200	Weak transcription	Small Intestine	intestine
42	chr13:79894400-79909200	Weak transcription	Brain Germinal Matrix	brain
43	chr13:79894400-79910600	Weak transcription	Thymus	Thymus
44	chr13:79894400-79950200	Weak transcription	Stomach Mucosa	stomach
45	chr13:79895200-79909400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr13:79895800-79905200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr13:79896000-79908000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:79896000-79908000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr13:79896000-79910600	Weak transcription	Aorta	Aorta
50	chr13:79896200-79907200	Weak transcription	HUVEC	blood vessel

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