Variant report

Variant	rs1524530
Chromosome Location	chr7:27620780-27620781
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	chr7:27353470..27355486-chr7:27620520..27622885,2	MCF-7	breast:

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1005128	1.00[ASN][1000 genomes]
rs1009252	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1014373	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1015750	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1030003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10447552	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1052724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1052741	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10807841	1.00[ASN][1000 genomes]
rs10951169	1.00[ASN][1000 genomes]
rs10951171	1.00[ASN][1000 genomes]
rs10951172	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10951175	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10951176	1.00[JPT][hapmap]
rs1111647	1.00[ASN][1000 genomes]
rs11526176	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11767188	1.00[ASN][1000 genomes]
rs12155430	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12164139	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12530626	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12535844	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12537499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12540276	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12665991	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12667235	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12667610	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12668430	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12670415	0.93[ASN][1000 genomes]
rs12700813	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12700815	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12700817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12700819	0.90[ASN][1000 genomes]
rs12700822	0.90[ASN][1000 genomes]
rs12700826	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13226102	0.83[ASN][1000 genomes]
rs13227873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13237776	1.00[JPT][hapmap]
rs13242248	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13244903	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13246464	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13308974	0.83[ASN][1000 genomes]
rs1357760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404276	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1404278	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1524526	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1524531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524532	1.00[ASN][1000 genomes]
rs1524533	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1554641	1.00[ASN][1000 genomes]
rs1608664	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17155546	1.00[JPT][hapmap]
rs1851911	0.90[ASN][1000 genomes]
rs1851912	0.90[ASN][1000 genomes]
rs1851913	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1880370	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1980329	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1986243	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041714	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2080245	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2080246	1.00[ASN][1000 genomes]
rs2091171	1.00[ASN][1000 genomes]
rs2098315	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2098316	1.00[ASN][1000 genomes]
rs2110526	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2110528	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2391443	1.00[ASN][1000 genomes]
rs2391452	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2391453	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs28416309	0.96[ASN][1000 genomes]
rs28429439	1.00[ASN][1000 genomes]
rs34886410	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847001	1.00[ASN][1000 genomes]
rs3925338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4140899	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs42085	1.00[JPT][hapmap]
rs42099	1.00[JPT][hapmap]
rs4348389	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4719898	1.00[ASN][1000 genomes]
rs4719899	0.82[ASN][1000 genomes]
rs4719900	1.00[ASN][1000 genomes]
rs4719902	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4722719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4722724	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4722728	1.00[JPT][hapmap]
rs58747588	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6415251	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6462026	1.00[ASN][1000 genomes]
rs6462029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6462031	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6462032	1.00[ASN][1000 genomes]
rs6462034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6462036	0.93[ASN][1000 genomes]
rs6462037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6462038	1.00[JPT][hapmap]
rs6945993	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6946075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947731	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6948814	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6949496	1.00[ASN][1000 genomes]
rs6955074	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6956484	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957674	1.00[ASN][1000 genomes]
rs6958747	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6959126	0.85[ASN][1000 genomes]
rs6959495	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6960834	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6961429	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6963421	1.00[JPT][hapmap]
rs6963585	1.00[ASN][1000 genomes]
rs6964190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6966918	1.00[ASN][1000 genomes]
rs6970104	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6974052	1.00[ASN][1000 genomes]
rs6974387	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6974932	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6980382	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs723699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7455882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759269	1.00[ASN][1000 genomes]
rs7778320	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7779240	1.00[ASN][1000 genomes]
rs7780431	1.00[ASN][1000 genomes]
rs7783447	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7789788	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7794292	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7805086	0.83[EUR][1000 genomes]
rs7806605	1.00[ASN][1000 genomes]
rs7806812	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7811436	0.93[ASN][1000 genomes]
rs940525	1.00[ASN][1000 genomes]
rs940526	1.00[ASN][1000 genomes]
rs9639552	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9639553	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9639560	1.00[ASN][1000 genomes]
rs978447	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs986706	1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1524530	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27559400-27627800	Weak transcription	Psoas Muscle	Psoas
2	chr7:27582400-27650800	Weak transcription	Left Ventricle	heart
3	chr7:27600600-27645600	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:27603000-27626400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:27603200-27631800	Weak transcription	Primary T cells from cord blood	blood
6	chr7:27603600-27626400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr7:27605200-27624400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:27605800-27645800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:27609400-27632600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:27609400-27651000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:27615600-27621800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:27615600-27626400	Weak transcription	Ovary	ovary
13	chr7:27615600-27626400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:27615600-27657800	Weak transcription	Aorta	Aorta
15	chr7:27616000-27626600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:27616000-27631600	Weak transcription	Adipose Nuclei	Adipose
17	chr7:27616000-27632800	Weak transcription	HUVEC	blood vessel
18	chr7:27616000-27643400	Weak transcription	Fetal Lung	lung
19	chr7:27616000-27650800	Weak transcription	Fetal Kidney	kidney
20	chr7:27617600-27633000	Weak transcription	A549	lung
21	chr7:27618400-27645000	Weak transcription	Fetal Intestine Large	intestine
22	chr7:27619400-27624800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr7:27619600-27634800	Weak transcription	Fetal Intestine Small	intestine
24	chr7:27619600-27635600	Weak transcription	Liver	Liver
25	chr7:27619800-27639800	Weak transcription	HepG2	liver
26	chr7:27619800-27643400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:27620400-27620800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:27620400-27621200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:27620600-27621000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:27620600-27621000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:27620600-27621000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:27620600-27621000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links