Variant report

Variant	rs1465778
Chromosome Location	chr15:31621321-31621322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:31618168..31621382-chr15:31631982..31634646,4	MCF-7	breast:
2	chr15:31618838..31621702-chr15:31631313..31632972,2	MCF-7	breast:
3	chr15:31608249..31610861-chr15:31620080..31623099,3	K562	blood:
4	chr15:31608249..31610861-chr15:31620873..31623099,2	K562	blood:
5	chr15:31507074..31509248-chr15:31619187..31621529,2	MCF-7	breast:
6	chr15:31618253..31621608-chr15:31655043..31658553,3	K562	blood:

Variant related genes	Relation type
ENSG00000169926	Chromatin interaction
ENSG00000259448	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11537749	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636034	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11636159	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34693358	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779861	0.81[GIH][hapmap]
rs4779862	0.81[GIH][hapmap]
rs58566807	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59569306	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61036010	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7167092	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9920754	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv456747	chr15:31537496-31637996	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv568772	chr15:31537496-31637996	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv1839818	chr15:31594828-31637996	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv542318	chr15:31601016-31628938	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1050482	chr15:31601016-31672921	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv542319	chr15:31605961-31628938	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1048082	chr15:31610245-31667000	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
16	nsv1045944	chr15:31610245-31672921	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
17	nsv516681	chr15:31616674-31675453	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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	13 gene(s)	inside rSNPs	diseases
18	nsv903841	chr15:31616674-31697242	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
19	esv3322979	chr15:31617060-31621658	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv827280	chr15:31617536-31621947	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	esv3416843	chr15:31617660-31621758	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
22	esv1824341	chr15:31617859-31621321	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
23	esv3487683	chr15:31617885-31622158	Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
24	esv3487684	chr15:31617885-31622158	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
25	nsv568786	chr15:31618113-31621321	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
26	esv3358300	chr15:31618685-31622033	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
27	esv1823395	chr15:31618900-31621321	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
28	nsv903842	chr15:31621321-31697242	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
29	nsv456748	chr15:31621321-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
30	nsv568801	chr15:31621321-31697642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1465778	SNORD115-40	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31617200-31621800	Active TSS	Left Ventricle	heart
2	chr15:31617400-31621800	Active TSS	GM12878-XiMat	blood
3	chr15:31617400-31622000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr15:31617400-31622000	Active TSS	Esophagus	oesophagus
5	chr15:31617400-31622400	Active TSS	Gastric	stomach
6	chr15:31617600-31621400	Active TSS	Spleen	Spleen
7	chr15:31617600-31621600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:31617600-31621600	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr15:31617600-31621800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:31617600-31621800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr15:31617600-31621800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:31617600-31621800	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr15:31617600-31621800	Active TSS	Lung	lung
14	chr15:31617600-31621800	Active TSS	Small Intestine	intestine
15	chr15:31617600-31621800	Active TSS	NHLF	lung
16	chr15:31617600-31622000	Active TSS	Brain Angular Gyrus	brain
17	chr15:31617600-31622000	Active TSS	Fetal Intestine Small	intestine
18	chr15:31617600-31622200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:31617600-31622200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr15:31617600-31622200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr15:31617800-31621400	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr15:31617800-31621400	Active TSS	Fetal Kidney	kidney
23	chr15:31617800-31621400	Active TSS	HSMMtube	muscle
24	chr15:31617800-31621600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:31617800-31621600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:31617800-31621600	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr15:31617800-31621600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:31617800-31621600	Active TSS	NHDF-Ad	bronchial
29	chr15:31617800-31621800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr15:31617800-31621800	Active TSS	H1 Cell Line	embryonic stem cell
31	chr15:31617800-31621800	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr15:31617800-31621800	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr15:31617800-31621800	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr15:31617800-31621800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:31617800-31621800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:31617800-31621800	Active TSS	Primary T cells from cord blood	blood
37	chr15:31617800-31621800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr15:31617800-31621800	Active TSS	Colon Smooth Muscle	Colon
39	chr15:31617800-31621800	Active TSS	Fetal Intestine Large	intestine
40	chr15:31617800-31621800	Active TSS	Hela-S3	cervix
41	chr15:31617800-31621800	Active TSS	HepG2	liver
42	chr15:31617800-31621800	Active TSS	NHEK	skin
43	chr15:31617800-31622000	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr15:31617800-31622000	Active TSS	Brain Cingulate Gyrus	brain
45	chr15:31617800-31622000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:31617800-31622000	Active TSS	Fetal Brain Female	brain
47	chr15:31617800-31622000	Active TSS	Pancreas	Pancrea
48	chr15:31617800-31622200	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr15:31617800-31622600	Active TSS	Rectal Smooth Muscle	rectum
50	chr15:31618000-31621800	Active TSS	ES-I3 Cell Line	embryonic stem cell

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