Variant report

Variant	rs2929508
Chromosome Location	chr15:72246964-72246965
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1074330	0.84[CEU][hapmap]
rs10851847	0.81[AMR][1000 genomes]
rs10851850	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11072339	0.85[CEU][hapmap]
rs11072349	0.84[EUR][1000 genomes]
rs11072350	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11630170	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11630611	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11631650	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11633167	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634608	0.93[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11639282	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12050794	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12148078	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12439494	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12592044	0.84[CEU][hapmap]
rs12901886	0.84[CEU][hapmap]
rs12902006	0.84[CEU][hapmap]
rs12912771	0.86[EUR][1000 genomes]
rs12914070	0.84[CEU][hapmap]
rs12916951	0.84[CEU][hapmap]
rs13858	0.86[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1481860	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1481861	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1481862	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16956273	0.92[CEU][hapmap]
rs16956369	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2034879	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs2128112	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2278987	0.93[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2306489	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306576	0.93[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2415120	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs2415121	0.84[EUR][1000 genomes]
rs2415126	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2415128	0.86[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2415130	0.80[EUR][1000 genomes]
rs2723342	0.83[CEU][hapmap]
rs28650442	0.88[EUR][1000 genomes]
rs28717020	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899775	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899776	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929509	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2929510	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2929511	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929513	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929517	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2929518	0.93[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap]
rs2929525	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929526	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2929527	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2929528	0.86[EUR][1000 genomes]
rs2929532	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2930069	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957361	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957365	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957368	0.85[EUR][1000 genomes]
rs2957373	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2957724	0.93[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957725	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2957728	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957734	0.92[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957735	0.93[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957736	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957737	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2957740	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957742	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957743	0.81[AMR][1000 genomes]
rs2957745	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957746	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957750	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759820	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784310	0.86[CEU][hapmap]
rs3784313	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4238449	0.82[CEU][hapmap]
rs4454922	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4511483	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4526973	0.87[EUR][1000 genomes]
rs4776586	0.85[CEU][hapmap]
rs4777466	0.84[EUR][1000 genomes]
rs4777485	0.82[EUR][1000 genomes]
rs55679065	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59975112	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62023343	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6494973	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6494975	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6494990	0.83[EUR][1000 genomes]
rs6494992	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7162299	0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7164780	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7170456	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7172158	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7172309	0.84[CEU][hapmap]
rs7173626	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7175197	0.82[EUR][1000 genomes]
rs7175373	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7175792	0.93[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7177242	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7183055	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7183748	0.82[EUR][1000 genomes]
rs7403191	0.82[EUR][1000 genomes]
rs7496582	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7497104	0.93[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs8023788	0.82[EUR][1000 genomes]
rs8025939	0.82[EUR][1000 genomes]
rs8027164	0.93[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8028115	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8030815	0.93[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8032222	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8036307	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8037381	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8040216	0.90[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040828	0.82[EUR][1000 genomes]
rs8178	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs8182011	0.82[EUR][1000 genomes]
rs8557	0.86[CEU][hapmap]
rs9120	0.85[CEU][hapmap]
rs9302260	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs982752	1.00[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
5	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
6	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
7	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
8	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
9	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
10	nsv457197	chr15:72203517-72296328	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv569910	chr15:72203517-72296328	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv569911	chr15:72203517-72305982	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv457198	chr15:72203517-72325595	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv569912	chr15:72203517-72325595	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2929508	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72192400-72249400	Weak transcription	NHLF	lung
2	chr15:72225000-72249400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:72225000-72249600	Weak transcription	NH-A	brain
4	chr15:72225000-72255400	Weak transcription	Left Ventricle	heart
5	chr15:72225000-72259800	Weak transcription	Brain Anterior Caudate	brain
6	chr15:72225000-72263600	Weak transcription	Fetal Stomach	stomach
7	chr15:72225000-72267600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:72225000-72281600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:72225000-72282000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:72225000-72305200	Weak transcription	Psoas Muscle	Psoas
11	chr15:72225000-72305600	Weak transcription	Gastric	stomach
12	chr15:72225200-72259200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:72225200-72265000	Weak transcription	Fetal Kidney	kidney
14	chr15:72225800-72270200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:72226600-72281800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:72226800-72271200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr15:72226800-72343600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:72227000-72252200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:72227200-72252200	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:72227200-72254000	Weak transcription	Fetal Intestine Large	intestine
21	chr15:72227400-72253800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:72227600-72265800	Weak transcription	HSMMtube	muscle
23	chr15:72227600-72281600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:72227600-72281800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:72227800-72250400	Weak transcription	Adipose Nuclei	Adipose
26	chr15:72227800-72251000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:72227800-72252200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:72227800-72281600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:72227800-72326200	Weak transcription	Fetal Brain Male	brain
30	chr15:72228200-72265600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr15:72228200-72268200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:72228600-72251800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:72228600-72258800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:72228800-72251600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:72228800-72261400	Weak transcription	Ovary	ovary
36	chr15:72228800-72268000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:72228800-72279600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr15:72228800-72281600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:72230600-72291000	Weak transcription	Primary B cells from cord blood	blood
40	chr15:72232800-72255800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:72232800-72264800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:72233400-72261400	Weak transcription	GM12878-XiMat	blood
43	chr15:72233400-72267400	Weak transcription	HMEC	breast
44	chr15:72233400-72267800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:72233400-72268200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:72237800-72255400	Weak transcription	Right Ventricle	heart
47	chr15:72238200-72247600	Weak transcription	NHDF-Ad	bronchial
48	chr15:72238200-72250800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:72240000-72268200	Weak transcription	Esophagus	oesophagus
50	chr15:72240200-72282200	Weak transcription	Aorta	Aorta

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