Variant report

Variant	rs1867092
Chromosome Location	chr15:100018188-100018189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99976307..99978594-chr15:100018036..100019822,2	MCF-7	breast:
2	chr15:99981781..99983657-chr15:100018041..100019744,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1020255	0.94[EUR][1000 genomes]
rs1020256	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10902545	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10902546	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10902547	0.87[EUR][1000 genomes]
rs11630522	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11632243	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11632288	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11632631	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11633249	1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs11637736	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903278	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12904009	0.93[EUR][1000 genomes]
rs12909847	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1442645	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1867091	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867093	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1867094	0.96[CEU][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2119941	0.94[EUR][1000 genomes]
rs34457611	0.97[EUR][1000 genomes]
rs34666134	0.88[EUR][1000 genomes]
rs34974576	0.86[EUR][1000 genomes]
rs35015146	0.90[EUR][1000 genomes]
rs35395415	0.90[EUR][1000 genomes]
rs36112416	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4965251	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56159751	0.93[EUR][1000 genomes]
rs56197704	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7167860	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172915	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7180712	0.86[EUR][1000 genomes]
rs7181817	0.94[EUR][1000 genomes]
rs920657	0.80[CEU][hapmap];0.85[JPT][hapmap]

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	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
8	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv1050527	chr15:99983054-100035436	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1867092	MCTP2	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100008200-100020600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:100012400-100018200	Enhancers	Stomach Mucosa	stomach
3	chr15:100012400-100018600	Enhancers	Spleen	Spleen
4	chr15:100012400-100018800	Enhancers	Right Atrium	heart
5	chr15:100012600-100018600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr15:100012600-100019000	Enhancers	Fetal Heart	heart
7	chr15:100012800-100018800	Enhancers	Fetal Lung	lung
8	chr15:100013000-100018600	Enhancers	Right Ventricle	heart
9	chr15:100013000-100018800	Enhancers	Fetal Muscle Trunk	muscle
10	chr15:100013000-100019400	Enhancers	Fetal Thymus	thymus
11	chr15:100013200-100019000	Enhancers	Fetal Muscle Leg	muscle
12	chr15:100013600-100018400	Enhancers	Placenta	Placenta
13	chr15:100013600-100018400	Enhancers	Lung	lung
14	chr15:100013800-100018200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:100013800-100018200	Enhancers	HMEC	breast
16	chr15:100014000-100018600	Enhancers	HSMMtube	muscle
17	chr15:100014000-100019200	Enhancers	Fetal Stomach	stomach
18	chr15:100014800-100018800	Enhancers	Left Ventricle	heart
19	chr15:100014800-100020200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr15:100014800-100026800	Weak transcription	Aorta	Aorta
21	chr15:100015200-100018600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:100015400-100018200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:100015400-100018400	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr15:100015600-100018400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr15:100015600-100018600	Enhancers	NHDF-Ad	bronchial
26	chr15:100015600-100018800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr15:100015800-100019000	Enhancers	Dnd41	blood
28	chr15:100016000-100019000	Enhancers	Primary B cells from cord blood	blood
29	chr15:100016000-100019000	Enhancers	Primary B cells from peripheral blood	blood
30	chr15:100016000-100019000	Enhancers	Thymus	Thymus
31	chr15:100016200-100018200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:100016200-100018200	Enhancers	Fetal Intestine Large	intestine
33	chr15:100016200-100018200	Enhancers	HUVEC	blood vessel
34	chr15:100016200-100019000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:100016200-100019600	Enhancers	Primary hematopoietic stem cells	blood
36	chr15:100016400-100018400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr15:100016400-100018600	Enhancers	Brain Cingulate Gyrus	brain
38	chr15:100016400-100018800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr15:100016400-100018800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr15:100016600-100018600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr15:100016600-100018800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:100016600-100018800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr15:100016800-100018200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:100016800-100018200	Enhancers	Esophagus	oesophagus
45	chr15:100016800-100018400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:100016800-100018400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr15:100016800-100018400	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr15:100016800-100018400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:100016800-100018600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr15:100017000-100018400	Enhancers	Gastric	stomach

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