Variant report

Variant	rs5015024
Chromosome Location	chr15:74704588-74704589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:74702401-74714587	U87	brain:	n/a	n/a
2	POLR2A	chr15:74698747-74718413	GM18505	blood:	n/a	n/a
3	NFATC1	chr15:74703670-74704802	GM12878	blood:	n/a	n/a
4	NFATC1	chr15:74704328-74704888	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:74702740-74705202	U87	brain:	n/a	n/a
6	EBF1	chr15:74704567-74704592	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:74704579-74704700	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:74702432-74704818	GM18526	blood:	n/a	n/a
9	POLR2A	chr15:74702264-74704954	GM12892	blood:	n/a	n/a
10	POLR2A	chr15:74699045-74704897	GM19193	blood:	n/a	n/a
11	POLR2A	chr15:74702408-74704807	GM15510	blood:	n/a	n/a
12	POLR2A	chr15:74698891-74704906	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:74699031-74704829	GM18951	blood:	n/a	n/a
14	POLR2A	chr15:74702282-74710077	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:74702332-74704838	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:74699081-74705078	GM12892	blood:	n/a	n/a
17	POLR2A	chr15:74697925-74718369	GM12891	blood:	n/a	n/a
18	POLR2A	chr15:74697998-74704828	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:74698793-74725579	GM12878	blood:	n/a	n/a
20	POLR2A	chr15:74703016-74704813	GM19099	blood:	n/a	n/a
21	POLR2A	chr15:74702280-74704867	GM12892	blood:	n/a	n/a
22	POLR2A	chr15:74702280-74704989	GM12892	blood:	n/a	n/a
23	POLR2A	chr15:74704246-74704715	GM12891	blood:	n/a	n/a
24	POLR2A	chr15:74702356-74704864	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SEMA7A	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12441582	0.82[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs28362930	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35163659	0.84[AMR][1000 genomes]
rs4243086	0.85[GIH][hapmap];0.90[MEX][hapmap]
rs7175229	0.85[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][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	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
3	nsv904352	chr15:74638965-74715205	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	23 gene(s)	inside rSNPs	diseases
4	nsv904353	chr15:74697084-74716609	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv904354	chr15:74697084-74722924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv904355	chr15:74697084-74728149	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
7	nsv904356	chr15:74697084-74729603	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv569974	chr15:74701200-74727113	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5015024	SCAMP5	cis	lymphoblastoid	seeQTL
rs5015024	NRG4	cis	parietal	SCAN
rs5015024	SCAMP5	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74696200-74710400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:74696200-74711400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr15:74696200-74712600	Weak transcription	Right Atrium	heart
4	chr15:74696400-74707000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:74696400-74712200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:74696600-74706200	Weak transcription	Primary T cells from cord blood	blood
7	chr15:74696800-74709400	Weak transcription	Left Ventricle	heart
8	chr15:74697000-74705400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:74697000-74712400	Weak transcription	Fetal Heart	heart
10	chr15:74697000-74712600	Weak transcription	Fetal Lung	lung
11	chr15:74697200-74705200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr15:74699600-74706200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:74699600-74716600	Weak transcription	Fetal Kidney	kidney
14	chr15:74699800-74704600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:74700000-74713800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:74700200-74707000	Weak transcription	Esophagus	oesophagus
17	chr15:74700200-74707400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:74700200-74708400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:74700200-74708400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:74700200-74711200	Weak transcription	Fetal Intestine Large	intestine
21	chr15:74700400-74708000	Genic enhancers	HSMM	muscle
22	chr15:74700400-74710800	Weak transcription	Ovary	ovary
23	chr15:74700600-74712200	Weak transcription	Fetal Brain Male	brain
24	chr15:74700800-74712400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:74701000-74708000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:74701000-74708400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:74701200-74704800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:74701200-74706800	Strong transcription	Thymus	Thymus
29	chr15:74701200-74714600	Genic enhancers	Spleen	Spleen
30	chr15:74701400-74705000	Strong transcription	Fetal Brain Female	brain
31	chr15:74701400-74706800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:74701400-74712600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:74701600-74706600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:74701600-74706800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr15:74701600-74707200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr15:74701600-74707600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr15:74701600-74709200	Strong transcription	NHLF	lung
38	chr15:74701600-74709600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:74701800-74707800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:74701800-74708000	Strong transcription	HMEC	breast
41	chr15:74702000-74705400	Strong transcription	Fetal Thymus	thymus
42	chr15:74702000-74710800	Strong transcription	Brain Germinal Matrix	brain
43	chr15:74702000-74712400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr15:74702200-74704600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:74702200-74710800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:74702200-74710800	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr15:74702200-74715000	Weak transcription	Colonic Mucosa	Colon
48	chr15:74702400-74704600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:74702400-74704800	Strong transcription	Brain Hippocampus Middle	brain
50	chr15:74702400-74704800	Genic enhancers	Fetal Muscle Trunk	muscle

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