Variant report

Variant	rs2293320
Chromosome Location	chr15:31235575-31235576
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31234145..31235781-chr15:31240039..31242317,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10163148	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10519726	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs11070678	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070718	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs1133642	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs11638295	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs11852466	0.83[CHB][hapmap]
rs12437580	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12441318	0.85[CHB][hapmap]
rs12442333	0.82[CHB][hapmap]
rs12443369	0.82[EUR][1000 genomes]
rs12901022	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs12906480	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907055	0.80[ASN][1000 genomes]
rs1404467	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1404468	0.92[CHB][hapmap]
rs1404469	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs1474381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1474382	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1524876	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs16956341	0.83[CHB][hapmap]
rs16956362	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs16956366	0.83[CHB][hapmap]
rs16956414	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs16956422	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs17815804	0.88[CHD][hapmap]
rs1880499	0.92[CHB][hapmap]
rs2042613	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2113945	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs2113946	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2140735	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2272218	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2272219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2293319	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2339048	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28693590	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2873	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs28881289	0.97[ASN][1000 genomes]
rs2949567	0.82[ASN][1000 genomes]
rs2949568	0.82[GIH][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes]
rs2949569	0.92[CHB][hapmap];0.84[CHD][hapmap]
rs2949570	0.92[CHB][hapmap]
rs2949572	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2949573	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2949575	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2949576	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2949577	0.92[CHB][hapmap]
rs2949578	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2955783	0.92[CHB][hapmap]
rs2955787	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2955790	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2955791	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2955795	0.82[ASN][1000 genomes]
rs2955796	0.85[CHB][hapmap]
rs2959034	0.90[AMR][1000 genomes]
rs2959039	0.85[CHB][hapmap]
rs2959047	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2959049	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2959050	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2959051	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35162264	0.80[ASN][1000 genomes]
rs35497908	0.97[ASN][1000 genomes]
rs3743231	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3784588	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs4779796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4779797	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6493358	0.83[CHB][hapmap]
rs71474640	0.88[EUR][1000 genomes]
rs7161812	1.00[CHB][hapmap]
rs7164530	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7164939	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7165798	0.92[CHB][hapmap]
rs7169064	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7170710	0.92[CHB][hapmap]
rs7170772	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7175256	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7175951	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7176351	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7178375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7178533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7182143	0.92[CHB][hapmap]
rs7183880	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798101	0.85[CHB][hapmap]
rs8040989	0.92[CHB][hapmap]
rs8041717	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs871312	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs872843	0.83[CHB][hapmap]
rs964925	0.84[CHD][hapmap]
rs9806159	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv533434	chr15:30938215-31244225	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
7	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
10	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
11	nsv1039037	chr15:31140415-31277268	Strong transcription ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv542309	chr15:31140415-31277268	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv521842	chr15:31140700-31272670	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv903834	chr15:31179534-31293774	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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 miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
18	esv3431290	chr15:31234652-31236255	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2293320	MTMR10	cis	multi-tissue	Pritchard
rs2293320	SNORD115-35	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31200400-31242200	Strong transcription	Primary T cells from cord blood	blood
2	chr15:31200600-31254800	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr15:31201200-31241400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:31215200-31238600	Weak transcription	Fetal Heart	heart
5	chr15:31215200-31241000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:31215800-31236600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:31216000-31241600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:31216600-31245800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:31221000-31246800	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:31222600-31241000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:31223200-31237600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:31223800-31239200	Weak transcription	Fetal Brain Male	brain
13	chr15:31225400-31246200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr15:31225400-31255800	Strong transcription	Fetal Intestine Large	intestine
15	chr15:31225600-31241000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:31225600-31246000	Strong transcription	Placenta	Placenta
17	chr15:31225600-31246200	Strong transcription	Adipose Nuclei	Adipose
18	chr15:31225600-31253800	Strong transcription	Dnd41	blood
19	chr15:31225800-31241400	Strong transcription	Fetal Muscle Leg	muscle
20	chr15:31225800-31245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:31225800-31246200	Strong transcription	GM12878-XiMat	blood
22	chr15:31225800-31256000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:31226000-31241400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:31226000-31245400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:31226000-31246000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:31226000-31255800	Strong transcription	Fetal Stomach	stomach
27	chr15:31226000-31258800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr15:31226200-31236400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:31226200-31237200	Strong transcription	Fetal Lung	lung
30	chr15:31226200-31246400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:31226200-31246800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:31226200-31269200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:31226400-31241400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:31226400-31260800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:31226600-31236000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:31226600-31245400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:31226600-31246000	Strong transcription	Ovary	ovary
38	chr15:31226600-31254400	Strong transcription	Fetal Thymus	thymus
39	chr15:31226600-31255200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:31226800-31244200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:31226800-31245600	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr15:31227000-31269600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr15:31227200-31236200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:31227200-31255800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:31227200-31258800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:31227400-31241800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr15:31228000-31246000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:31228200-31240200	Strong transcription	Left Ventricle	heart
49	chr15:31228200-31246000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr15:31228400-31236200	Strong transcription	NHEK	skin

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