Variant report

Variant	rs2899773
Chromosome Location	chr15:72196804-72196805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10518979	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1074330	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072338	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072339	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072346	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11852789	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11853268	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050895	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12439900	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12591426	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12592044	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12592364	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12593134	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12593908	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12595228	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12595464	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12899485	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12901580	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12901886	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12902006	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903484	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12903980	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906711	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12908300	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12908882	0.84[ASN][1000 genomes]
rs12911154	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12913042	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12914070	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12916694	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12916951	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12917428	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1384007	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1481860	0.80[EUR][1000 genomes]
rs1481861	0.81[EUR][1000 genomes]
rs16956241	0.86[EUR][1000 genomes]
rs16956302	0.90[EUR][1000 genomes]
rs16956328	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16956381	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16956444	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16956452	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2035379	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2054601	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2200056	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246225	0.81[ASN][1000 genomes]
rs2279283	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306488	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306490	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2415130	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2625530	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2723342	0.81[EUR][1000 genomes]
rs2723343	0.80[EUR][1000 genomes]
rs2723356	0.81[EUR][1000 genomes]
rs2742323	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2957725	0.80[EUR][1000 genomes]
rs2957737	0.80[EUR][1000 genomes]
rs34085279	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34137768	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34189331	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34514871	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35021156	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35112434	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35115747	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35167572	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35186252	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35258998	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35673773	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4131630	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4238447	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4238449	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4411469	0.86[ASN][1000 genomes]
rs4445848	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4776579	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4776581	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776584	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4776586	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4777464	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4777467	0.87[EUR][1000 genomes]
rs4777469	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4777471	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4777474	0.99[ASN][1000 genomes]
rs4777477	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4777478	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4777480	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4777484	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4777489	0.86[ASN][1000 genomes]
rs55854204	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62023342	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62025574	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71395051	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170461	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7170754	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7172309	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7177242	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7183748	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7183749	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7403191	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8025504	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028532	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8032038	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9120	0.83[EUR][1000 genomes]
rs972028	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs972029	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][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	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv569906	chr15:72126034-72218036	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv516871	chr15:72126034-72325595	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv904336	chr15:72145937-72329906	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv569907	chr15:72154000-72215065	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv569908	chr15:72154000-72218036	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv457195	chr15:72177659-72250741	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv569909	chr15:72177659-72250741	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2899773	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72142600-72199200	Weak transcription	Hela-S3	cervix
2	chr15:72144600-72223400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr15:72161000-72211000	Weak transcription	Small Intestine	intestine
4	chr15:72164000-72218400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:72167000-72197800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:72173000-72200600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:72185600-72198600	Weak transcription	A549	lung
8	chr15:72189200-72198000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:72189400-72197400	Strong transcription	Adipose Nuclei	Adipose
10	chr15:72189400-72197400	Strong transcription	Placenta	Placenta
11	chr15:72189400-72197600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:72189400-72197800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:72189800-72197200	Strong transcription	Liver	Liver
14	chr15:72189800-72197400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:72190800-72203800	Weak transcription	HMEC	breast
16	chr15:72190800-72206400	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:72191000-72198600	Weak transcription	Fetal Brain Male	brain
18	chr15:72191000-72199200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:72191000-72222800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:72191200-72197800	Weak transcription	Right Ventricle	heart
21	chr15:72191200-72198600	Weak transcription	Brain Anterior Caudate	brain
22	chr15:72191200-72200800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:72191200-72206000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:72191200-72206000	Weak transcription	Ovary	ovary
25	chr15:72191200-72229600	Weak transcription	HUVEC	blood vessel
26	chr15:72191600-72198400	Weak transcription	Colonic Mucosa	Colon
27	chr15:72191600-72198600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:72191600-72208000	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:72192200-72198800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:72192400-72198200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:72192400-72199400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:72192400-72201000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:72192400-72201000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:72192400-72201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:72192400-72203000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:72192400-72205000	Weak transcription	GM12878-XiMat	blood
37	chr15:72192400-72208600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:72192400-72216000	Weak transcription	Fetal Intestine Large	intestine
39	chr15:72192400-72218400	Weak transcription	Esophagus	oesophagus
40	chr15:72192400-72218400	Weak transcription	Lung	lung
41	chr15:72192400-72218600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:72192400-72218800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:72192400-72222800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:72192400-72223400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:72192400-72223400	Weak transcription	NH-A	brain
46	chr15:72192400-72223600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:72192400-72224000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:72192400-72241200	Weak transcription	Brain Angular Gyrus	brain
49	chr15:72192400-72249400	Weak transcription	NHLF	lung
50	chr15:72192600-72198200	Weak transcription	Spleen	Spleen

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