Variant report

Variant	rs12439900
Chromosome Location	chr15:72373640-72373641
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 154 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs1037680	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10518979	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1074330	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072338	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072339	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072346	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630170	0.83[CEU][hapmap]
rs11633167	0.83[CEU][hapmap]
rs11634608	0.83[CEU][hapmap]
rs11852789	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11853101	0.84[EUR][1000 genomes]
rs11853268	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11858015	0.84[EUR][1000 genomes]
rs12050895	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12442886	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12591313	0.82[EUR][1000 genomes]
rs12591338	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs12591426	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12592044	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592364	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593134	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593908	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12595228	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12595464	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898585	0.84[AMR][1000 genomes]
rs12899485	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12901580	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901886	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12902006	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12902661	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12903484	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12903980	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904652	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs12906711	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12908300	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12908882	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911154	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12913042	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914070	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12916694	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12916951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917428	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384007	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1481860	0.83[EUR][1000 genomes]
rs1481861	0.82[EUR][1000 genomes]
rs16953769	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16956302	0.84[EUR][1000 genomes]
rs16956328	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16956381	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16956444	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16956452	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16956634	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs2035379	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054601	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2200056	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278987	0.82[CEU][hapmap]
rs2279283	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306488	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306490	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2415130	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2607090	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2625530	0.84[EUR][1000 genomes]
rs2856929	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2899773	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2912231	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2929508	0.85[CEU][hapmap]
rs2929518	0.83[CEU][hapmap]
rs2929528	0.82[EUR][1000 genomes]
rs2957368	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2957373	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2957724	0.83[CEU][hapmap]
rs2957725	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2957734	0.81[CEU][hapmap]
rs2957735	0.82[CEU][hapmap]
rs2957737	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34085279	0.86[ASN][1000 genomes]
rs34137768	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34189331	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34487006	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34514871	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35021156	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35112434	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35115747	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35167572	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35186252	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35206011	0.84[EUR][1000 genomes]
rs35258998	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35673773	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35713471	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3743224	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759900	0.88[CEU][hapmap]
rs3803471	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4131630	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238447	0.84[EUR][1000 genomes]
rs4238449	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4411469	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4445848	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776579	0.83[EUR][1000 genomes]
rs4776581	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4776584	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4776586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4776589	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4777464	0.83[EUR][1000 genomes]
rs4777467	0.81[EUR][1000 genomes]
rs4777469	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4777471	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4777474	0.90[ASN][1000 genomes]
rs4777477	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4777478	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4777480	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4777484	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4777485	0.85[EUR][1000 genomes]
rs4777489	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55854204	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60921026	0.88[ASN][1000 genomes]
rs62023342	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62025574	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6494975	0.88[CEU][hapmap]
rs6494990	0.83[EUR][1000 genomes]
rs6494992	0.88[CEU][hapmap]
rs713048	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs71395051	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7170461	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7170754	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7172309	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175792	0.83[CEU][hapmap]
rs7177242	0.88[CEU][hapmap]
rs7182776	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7183196	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs7183749	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72733369	0.82[EUR][1000 genomes]
rs8023703	0.81[ASN][1000 genomes]
rs8025504	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027164	0.83[CEU][hapmap]
rs8028115	0.83[CEU][hapmap]
rs8028532	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8030815	0.83[CEU][hapmap]
rs8032038	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8182011	0.85[EUR][1000 genomes]
rs8192364	0.81[EUR][1000 genomes]
rs8192386	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8192431	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs972028	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs972029	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv11550	chr15:72353301-72395288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv904337	chr15:72361942-72390515	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12439900	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72351200-72395800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:72353600-72379600	Weak transcription	Primary T cells from cord blood	blood
3	chr15:72354000-72378400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:72354400-72374800	Weak transcription	Psoas Muscle	Psoas
5	chr15:72355800-72376200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:72361600-72377400	Weak transcription	Fetal Intestine Small	intestine
7	chr15:72361600-72390600	Weak transcription	Aorta	Aorta
8	chr15:72361600-72391400	Weak transcription	Ovary	ovary
9	chr15:72367200-72407600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:72367800-72377400	Weak transcription	Fetal Stomach	stomach
11	chr15:72370000-72378400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:72370800-72374800	Weak transcription	Right Ventricle	heart
13	chr15:72370800-72378600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:72371200-72374600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:72371200-72377400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:72371400-72374400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:72371400-72376800	Weak transcription	Fetal Brain Female	brain
18	chr15:72371400-72379600	Weak transcription	Brain Anterior Caudate	brain
19	chr15:72372200-72378000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:72372200-72399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:72373600-72378400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:72373600-72394400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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