Variant report

Variant	rs39713
Chromosome Location	chr22:30343186-30343187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11549795	0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap]
rs11552852	0.82[EUR][1000 genomes]
rs1544429	0.95[EUR][1000 genomes]
rs1544430	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1544431	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1544433	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16988025	0.82[LWK][hapmap];0.86[MEX][hapmap];0.82[YRI][hapmap]
rs16988120	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16988143	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16988148	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16988149	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16988244	0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16988291	0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs16988303	0.94[YRI][hapmap];0.85[EUR][1000 genomes]
rs16988304	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs16988333	0.85[EUR][1000 genomes]
rs17648208	0.85[EUR][1000 genomes]
rs1807726	0.85[EUR][1000 genomes]
rs2105871	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2107674	0.80[EUR][1000 genomes]
rs2349228	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs249394	0.93[YRI][hapmap]
rs249403	1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap]
rs28265	0.89[YRI][hapmap]
rs36577	1.00[MEX][hapmap];0.85[TSI][hapmap]
rs36579	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36588	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36589	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36592	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36593	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36597	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36599	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36602	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36603	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36608	0.91[EUR][1000 genomes]
rs41278853	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41281623	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41281633	0.85[EUR][1000 genomes]
rs45629133	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4820823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55645000	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56332559	0.83[AMR][1000 genomes]
rs56392746	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56406718	0.85[EUR][1000 genomes]
rs57348516	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5752974	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5752977	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5752979	0.95[EUR][1000 genomes]
rs5763560	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5763568	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5763582	0.87[EUR][1000 genomes]
rs5763595	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58162368	0.85[EUR][1000 genomes]
rs5997539	0.93[EUR][1000 genomes]
rs6006276	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6006383	0.80[EUR][1000 genomes]
rs60759987	0.85[EUR][1000 genomes]
rs6519802	1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs6519805	0.85[EUR][1000 genomes]
rs7284365	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7284951	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7286205	1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs7286441	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7287233	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs737901	0.83[EUR][1000 genomes]
rs737938	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73883320	0.83[AMR][1000 genomes]
rs73883344	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73883349	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73883354	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883355	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883359	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73883360	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73883363	0.85[EUR][1000 genomes]
rs73883367	0.85[EUR][1000 genomes]
rs73883370	0.85[EUR][1000 genomes]
rs73883374	0.85[EUR][1000 genomes]
rs73883375	0.83[EUR][1000 genomes]
rs73883377	0.83[EUR][1000 genomes]
rs73883378	0.83[EUR][1000 genomes]
rs8141471	0.85[EUR][1000 genomes]
rs8142666	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1064489	chr22:30316627-30361881	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869764	chr22:30323649-30367813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1058511	chr22:30330447-30361881	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv2763694	chr22:30330459-30361881	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv588883	chr22:30333405-30365842	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs39713	MTMR3	cis	multi-tissue	Pritchard

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30311600-30343800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:30313000-30343800	Weak transcription	Fetal Stomach	stomach
3	chr22:30313600-30354200	Weak transcription	Small Intestine	intestine
4	chr22:30328400-30343600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr22:30328400-30351800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr22:30332600-30345000	Weak transcription	Pancreas	Pancrea
7	chr22:30332600-30347400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr22:30332800-30343800	Weak transcription	Adipose Nuclei	Adipose
9	chr22:30333600-30343600	Weak transcription	Brain Anterior Caudate	brain
10	chr22:30334200-30374800	Weak transcription	Thymus	Thymus
11	chr22:30339800-30343200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr22:30340000-30344000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr22:30340000-30344800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr22:30340000-30345000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr22:30340000-30345000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr22:30340000-30346800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr22:30340200-30343200	Weak transcription	NHLF	lung
18	chr22:30340200-30344200	Weak transcription	Right Ventricle	heart
19	chr22:30340200-30351000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr22:30340200-30355400	Weak transcription	Fetal Intestine Small	intestine
21	chr22:30340200-30374800	Weak transcription	Fetal Thymus	thymus
22	chr22:30340600-30347400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr22:30340600-30347600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr22:30340600-30347600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr22:30340600-30360400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr22:30340600-30370000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr22:30340600-30375000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr22:30340800-30343200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr22:30340800-30343400	Weak transcription	A549	lung
30	chr22:30340800-30343600	Weak transcription	HSMM	muscle
31	chr22:30340800-30343600	Weak transcription	HUVEC	blood vessel
32	chr22:30340800-30343800	Weak transcription	HMEC	breast
33	chr22:30340800-30350400	Weak transcription	Stomach Mucosa	stomach
34	chr22:30340800-30376000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr22:30341200-30343600	Weak transcription	HSMMtube	muscle
36	chr22:30341200-30345400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr22:30341200-30352200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr22:30341200-30353600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr22:30341400-30343800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr22:30341400-30344800	Weak transcription	Lung	lung
41	chr22:30341400-30346600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr22:30341400-30348000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr22:30341400-30351000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr22:30341400-30354400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr22:30341400-30355200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr22:30341600-30343200	Weak transcription	Fetal Brain Female	brain
47	chr22:30341600-30343800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr22:30341600-30344200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr22:30341600-30344600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr22:30341800-30343600	Enhancers	HUES48 Cell Line	embryonic stem cell

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