Variant report

Variant	rs6494990
Chromosome Location	chr15:72401074-72401075
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72401062..72403312-chr15:72406877..72409075,2	K562	blood:
2	chr15:72398664..72401840-chr15:72410348..72413852,3	K562	blood:
3	chr15:72398905..72401840-chr15:72409196..72411848,3	K562	blood:
4	chr15:72399406..72401734-chr15:72404487..72406226,2	K562	blood:

Variant related genes	Relation type
ENSG00000066933	Chromatin interaction
ENSG00000166192	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10518979	0.80[EUR][1000 genomes]
rs1074330	0.80[EUR][1000 genomes]
rs11072338	0.80[EUR][1000 genomes]
rs11072339	0.80[EUR][1000 genomes]
rs11072346	0.82[EUR][1000 genomes]
rs11072349	0.84[ASN][1000 genomes]
rs11072350	0.84[ASN][1000 genomes]
rs11630170	0.81[ASN][1000 genomes]
rs11631650	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11634608	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11639282	0.86[ASN][1000 genomes]
rs11852789	0.80[EUR][1000 genomes]
rs12050895	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12148078	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12439494	0.83[EUR][1000 genomes]
rs12439900	0.83[EUR][1000 genomes]
rs12591426	0.82[EUR][1000 genomes]
rs12592044	0.82[EUR][1000 genomes]
rs12592364	0.80[EUR][1000 genomes]
rs12593134	0.80[EUR][1000 genomes]
rs12593908	0.81[EUR][1000 genomes]
rs12595228	0.80[EUR][1000 genomes]
rs12595464	0.80[EUR][1000 genomes]
rs12901580	0.82[EUR][1000 genomes]
rs12901886	0.84[EUR][1000 genomes]
rs12902006	0.80[EUR][1000 genomes]
rs12903484	0.80[EUR][1000 genomes]
rs12906711	0.80[EUR][1000 genomes]
rs12908300	0.80[EUR][1000 genomes]
rs12911154	0.80[EUR][1000 genomes]
rs12912771	0.84[EUR][1000 genomes]
rs12914070	0.82[EUR][1000 genomes]
rs12916694	0.80[EUR][1000 genomes]
rs12916951	0.80[EUR][1000 genomes]
rs1384007	0.80[EUR][1000 genomes]
rs13858	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481860	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1481861	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1481862	0.83[EUR][1000 genomes]
rs16956444	0.80[EUR][1000 genomes]
rs16956452	0.80[EUR][1000 genomes]
rs2034879	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2035379	0.80[EUR][1000 genomes]
rs2200056	0.80[EUR][1000 genomes]
rs2278987	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306488	0.80[EUR][1000 genomes]
rs2306489	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2306490	0.80[EUR][1000 genomes]
rs2415128	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28717020	0.82[EUR][1000 genomes]
rs2899775	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2899776	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929508	0.83[EUR][1000 genomes]
rs2929509	0.82[EUR][1000 genomes]
rs2929511	0.81[EUR][1000 genomes]
rs2929513	0.82[EUR][1000 genomes]
rs2929517	0.84[EUR][1000 genomes]
rs2929525	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2929527	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929528	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929532	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2930069	0.82[EUR][1000 genomes]
rs2957361	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2957365	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2957368	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957373	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957375	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2957724	0.83[EUR][1000 genomes]
rs2957725	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957728	0.80[EUR][1000 genomes]
rs2957734	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2957735	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2957736	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2957737	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957740	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2957742	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2957743	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2957745	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2957746	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2957750	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35115747	0.80[EUR][1000 genomes]
rs35167572	0.83[EUR][1000 genomes]
rs35186252	0.83[EUR][1000 genomes]
rs35673773	0.83[EUR][1000 genomes]
rs3759820	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3759900	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4131630	0.83[EUR][1000 genomes]
rs4445848	0.83[EUR][1000 genomes]
rs4454922	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4776581	0.80[EUR][1000 genomes]
rs4776584	0.80[EUR][1000 genomes]
rs4776586	0.81[EUR][1000 genomes]
rs4777477	0.80[EUR][1000 genomes]
rs4777478	0.80[EUR][1000 genomes]
rs4777480	0.82[EUR][1000 genomes]
rs4777484	0.83[EUR][1000 genomes]
rs4777485	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55679065	0.86[ASN][1000 genomes]
rs55854204	0.81[EUR][1000 genomes]
rs59975112	0.88[ASN][1000 genomes]
rs6494975	0.81[EUR][1000 genomes]
rs6494992	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7162299	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164780	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7170456	0.82[ASN][1000 genomes]
rs7172158	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7172309	0.83[EUR][1000 genomes]
rs7175197	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7175373	0.82[EUR][1000 genomes]
rs7175792	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7177242	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7183055	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7183748	0.89[EUR][1000 genomes]
rs7183749	0.83[EUR][1000 genomes]
rs7403191	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8023788	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8025504	0.80[EUR][1000 genomes]
rs8025939	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8027164	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8028115	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8028532	0.83[EUR][1000 genomes]
rs8030815	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8032038	0.80[EUR][1000 genomes]
rs8037381	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040216	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8182011	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs982752	0.83[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
rs6494990	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 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	chr15:72391800-72401600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:72391800-72406600	Weak transcription	Ovary	ovary
11	chr15:72392600-72403000	Weak transcription	Fetal Intestine Small	intestine
12	chr15:72392600-72404000	Weak transcription	Fetal Stomach	stomach
13	chr15:72395800-72407800	Weak transcription	HMEC	breast
14	chr15:72395800-72409000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:72395800-72409200	Weak transcription	Gastric	stomach
16	chr15:72396000-72401400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:72396000-72401400	Weak transcription	Lung	lung
18	chr15:72396000-72402400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:72396000-72404200	Weak transcription	Osteobl	bone
20	chr15:72396000-72404600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:72396200-72404400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:72396400-72408800	Weak transcription	Right Ventricle	heart
23	chr15:72396600-72408200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:72397000-72404200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:72397200-72404200	Weak transcription	Fetal Lung	lung
26	chr15:72397400-72404200	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:72397800-72408200	Weak transcription	Brain Angular Gyrus	brain
28	chr15:72397800-72408200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:72399600-72404000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:72399800-72401400	Weak transcription	Left Ventricle	heart
31	chr15:72399800-72402400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:72399800-72404000	Weak transcription	Psoas Muscle	Psoas
33	chr15:72399800-72404200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:72399800-72404200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:72399800-72404800	Weak transcription	Fetal Heart	heart
36	chr15:72399800-72405800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:72399800-72408800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr15:72400600-72405400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr15:72401000-72402800	Weak transcription	A549	lung
40	chr15:72401000-72404000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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