Variant report

Variant	rs7164780
Chromosome Location	chr15:72402551-72402552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:72402454-72403355	A549	lung:	n/a	n/a
2	SP1	chr15:72402549-72403359	A549	lung:	n/a	n/a
3	TCF12	chr15:72402481-72403427	A549	lung:	n/a	n/a
4	EP300	chr15:72402551-72403286	A549	lung:	n/a	chr15:72402842-72402852

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72401062..72403312-chr15:72406877..72409075,2	K562	blood:

Variant related genes	Relation type
SENP8	TF binding region

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1000281	0.82[EUR][1000 genomes]
rs1035744	0.80[EUR][1000 genomes]
rs10851850	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072349	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072350	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630170	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11630611	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11631650	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11633167	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11634608	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634622	0.81[EUR][1000 genomes]
rs11637611	0.82[EUR][1000 genomes]
rs11639282	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12050794	0.84[EUR][1000 genomes]
rs12148078	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439494	0.81[EUR][1000 genomes]
rs12912771	0.82[EUR][1000 genomes]
rs13858	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1481860	0.83[EUR][1000 genomes]
rs1481861	0.82[EUR][1000 genomes]
rs1481862	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16956369	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2034879	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2052713	0.81[ASN][1000 genomes]
rs2128112	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2278987	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306489	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306576	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2415126	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2415128	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2415134	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28650442	0.82[EUR][1000 genomes]
rs28717020	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2899775	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899776	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2929508	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2929509	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2929510	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2929511	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2929513	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2929517	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2929525	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929526	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2929527	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2929528	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929532	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2930069	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2957361	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957365	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957368	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2957373	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2957724	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2957725	0.83[EUR][1000 genomes]
rs2957728	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957734	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957735	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957736	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957737	0.83[EUR][1000 genomes]
rs2957740	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957742	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957743	0.88[AMR][1000 genomes]
rs2957745	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957746	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957750	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34189331	0.80[EUR][1000 genomes]
rs35603965	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3759820	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3759900	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3784313	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4454922	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4506844	0.80[ASN][1000 genomes]
rs4777485	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55679065	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55763892	0.81[EUR][1000 genomes]
rs59975112	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62022788	0.80[EUR][1000 genomes]
rs62022789	0.80[EUR][1000 genomes]
rs62023343	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6494973	0.83[EUR][1000 genomes]
rs6494990	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494992	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6494997	0.81[EUR][1000 genomes]
rs7162299	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7170456	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172158	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173626	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7175197	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175373	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7175792	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7179427	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7179942	0.81[EUR][1000 genomes]
rs7183055	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7183810	0.80[EUR][1000 genomes]
rs7496582	0.82[EUR][1000 genomes]
rs7497104	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8023788	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8025939	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027164	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027647	0.81[EUR][1000 genomes]
rs8028115	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8030815	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8032222	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8036307	0.86[EUR][1000 genomes]
rs8037381	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8038007	0.80[EUR][1000 genomes]
rs8040216	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040828	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8182011	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8192362	0.81[ASN][1000 genomes]
rs9302260	0.86[EUR][1000 genomes]
rs982752	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
6	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
8	nsv869747	chr15:72372245-72403103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
10	nsv510665	chr15:72374862-72407548	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv511557	chr15:72386175-72408069	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv569929	chr15:72386349-72403001	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7164780	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72367200-72407600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:72375000-72408200	Weak transcription	Primary B cells from cord blood	blood
3	chr15:72379000-72407800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:72379800-72406200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:72380000-72407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:72389600-72403600	Weak transcription	Fetal Muscle Leg	muscle
7	chr15:72390400-72407600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:72391200-72404200	Weak transcription	HSMMtube	muscle
9	chr15:72391800-72406600	Weak transcription	Ovary	ovary
10	chr15:72392600-72403000	Weak transcription	Fetal Intestine Small	intestine
11	chr15:72392600-72404000	Weak transcription	Fetal Stomach	stomach
12	chr15:72395800-72407800	Weak transcription	HMEC	breast
13	chr15:72395800-72409000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:72395800-72409200	Weak transcription	Gastric	stomach
15	chr15:72396000-72404200	Weak transcription	Osteobl	bone
16	chr15:72396000-72404600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:72396200-72404400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:72396400-72408800	Weak transcription	Right Ventricle	heart
19	chr15:72396600-72408200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:72397000-72404200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:72397200-72404200	Weak transcription	Fetal Lung	lung
22	chr15:72397400-72404200	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:72397800-72408200	Weak transcription	Brain Angular Gyrus	brain
24	chr15:72397800-72408200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:72399600-72404000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:72399800-72404000	Weak transcription	Psoas Muscle	Psoas
27	chr15:72399800-72404200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:72399800-72404200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:72399800-72404800	Weak transcription	Fetal Heart	heart
30	chr15:72399800-72405800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:72399800-72408800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:72400600-72405400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:72401000-72402800	Weak transcription	A549	lung
34	chr15:72401000-72404000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:72401600-72409200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:72402400-72402600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:72402400-72402600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:72402400-72403600	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links