Variant report

Variant	rs12898794
Chromosome Location	chr15:74884447-74884448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:74884336-74884848	GM12891	blood:	n/a	n/a
2	POLR2A	chr15:74884109-74885093	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74884083..74885624-chr15:74906855..74909322,2	MCF-7	breast:
2	chr15:74883645..74887048-chr15:74903468..74905388,3	MCF-7	breast:
3	chr15:74831911..74834210-chr15:74881957..74884590,3	K562	blood:
4	chr15:74883904..74885997-chr15:74903287..74906186,2	MCF-7	breast:
5	chr15:74884059..74886045-chr15:74907649..74909590,2	K562	blood:
6	chr15:74882811..74885228-chr15:74890404..74892323,2	K562	blood:
7	chr15:74884292..74886470-chr15:74890567..74893261,3	MCF-7	breast:

No data

Variant related genes	Relation type
ARID3B	TF binding region
ENSG00000179361	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12914866	0.95[ASN][1000 genomes]
rs7496380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750607	0.82[ASW][hapmap];0.96[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv1812223	chr15:74869438-74948063	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv1814078	chr15:74884447-74948063	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12898794	SEMA7A	cis	cerebellum	SCAN
rs12898794	SCAMP5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74840600-74890400	Weak transcription	Stomach Mucosa	stomach
2	chr15:74845800-74890400	Weak transcription	A549	lung
3	chr15:74851800-74887800	Strong transcription	GM12878-XiMat	blood
4	chr15:74854800-74888600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr15:74857600-74888200	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr15:74857800-74887600	Strong transcription	Primary T cells from cord blood	blood
7	chr15:74859000-74888600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:74859600-74888000	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr15:74860400-74889000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:74860800-74888400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:74861200-74889800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:74863600-74890800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:74863800-74890400	Weak transcription	Psoas Muscle	Psoas
14	chr15:74864400-74887000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr15:74864400-74888400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:74866800-74890800	Weak transcription	Ovary	ovary
17	chr15:74868400-74886800	Strong transcription	Fetal Intestine Small	intestine
18	chr15:74873200-74884800	Weak transcription	HepG2	liver
19	chr15:74876600-74888800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:74877200-74888000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:74877400-74890400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:74877600-74887000	Strong transcription	Fetal Intestine Large	intestine
23	chr15:74877800-74888800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:74878000-74890200	Weak transcription	K562	blood
25	chr15:74878200-74887800	Strong transcription	Fetal Thymus	thymus
26	chr15:74878200-74888400	Strong transcription	Liver	Liver
27	chr15:74879800-74888000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:74881000-74886200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr15:74881000-74890400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr15:74881200-74888800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:74881200-74889600	Weak transcription	Fetal Heart	heart
32	chr15:74881200-74890400	Weak transcription	Fetal Kidney	kidney
33	chr15:74881200-74892200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:74881400-74888400	Strong transcription	Gastric	stomach
35	chr15:74881400-74889800	Strong transcription	Fetal Stomach	stomach
36	chr15:74881400-74890400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:74881400-74890400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:74881400-74890400	Weak transcription	Fetal Brain Male	brain
39	chr15:74881400-74892200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:74881600-74888200	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr15:74881600-74888400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr15:74881600-74890400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:74881800-74886000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:74881800-74888000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr15:74881800-74888000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr15:74881800-74888400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:74881800-74888400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:74881800-74888400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:74881800-74888400	Strong transcription	Brain Cingulate Gyrus	brain
50	chr15:74881800-74888800	Strong transcription	H1 Cell Line	embryonic stem cell

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