Variant report

Variant	rs12908814
Chromosome Location	chr15:75132490-75132491
allele	C/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	CTCF	chr15:75132480-75132630	SAEC	small airway:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
2	RAD21	chr15:75132383-75132700	H1-hESC	embryonic stem cell:	n/a	chr15:75132533-75132552
3	CTCF	chr15:75132440-75132590	K562	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
4	CTCF	chr15:75132355-75132629	H1-hESC	embryonic stem cell:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
5	CTCF	chr15:75132420-75132570	SAEC	small airway:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
6	CTCF	chr15:75132379-75132721	HepG2	liver:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
7	CTCF	chr15:75132450-75132636	MCF-7	breast:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
8	CTCF	chr15:75132420-75132570	HVMF	connective:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
9	RAD21	chr15:75132371-75132693	HepG2	liver:	n/a	chr15:75132533-75132552
10	CTCF	chr15:75132460-75132610	GM12870	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
11	CTCF	chr15:75132445-75132630	H1-hESC	embryonic stem cell:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
12	CTCF	chr15:75132465-75132666	GM13977	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
13	CTCF	chr15:75132400-75132550	A549	lung:	n/a	chr15:75132537-75132550
14	CTCF	chr15:75132480-75132630	GM12878	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
15	CTCF	chr15:75132469-75132617	MCF-7	breast:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
16	CTCF	chr15:75132467-75132627	Fibrobl	skin:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
17	RAD21	chr15:75132408-75132609	H1-hESC	embryonic stem cell:	n/a	chr15:75132533-75132552
18	CTCF	chr15:75132444-75132645	K562	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
19	CTCF	chr15:75132480-75132630	RPTEC	kidney:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
20	CTCF	chr15:75132420-75132570	HPF	lung:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
21	CTCF	chr15:75132440-75132590	GM12873	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
22	CTCF	chr15:75132480-75132630	GM06990	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
23	CTCF	chr15:75132460-75132610	HRPEpiC	eye:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
24	CTCF	chr15:75132387-75132659	K562	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
25	CTCF	chr15:75132460-75132610	GM12871	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
26	RAD21	chr15:75132471-75132631	Hela-S3	cervix:	n/a	chr15:75132533-75132552
27	CTCF	chr15:75132480-75132630	GM12864	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
28	CTCF	chr15:75132480-75132630	GM12873	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
29	RAD21	chr15:75132405-75132617	GM12878	blood:	n/a	chr15:75132533-75132552
30	CTCF	chr15:75132480-75132630	GM12869	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
31	RAD21	chr15:75132325-75132771	H1-hESC	embryonic stem cell:	n/a	chr15:75132533-75132552
32	SMC3	chr15:75132456-75132638	Hela-S3	cervix:	n/a	chr15:75132537-75132551
33	CTCF	chr15:75132440-75132590	AG04450	lung:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
34	CTCF	chr15:75132480-75132630	HepG2	liver:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
35	CTCF	chr15:75132400-75132550	NB4	blood:	n/a	chr15:75132537-75132550
36	CTCF	chr15:75132440-75132590	SK-N-SH_RA	brain:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
37	CTCF	chr15:75132404-75132704	GM12878	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
38	CTCF	chr15:75132476-75132638	GM10266	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
39	CTCF	chr15:75132460-75132610	HCFaa	heart:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
40	CTCF	chr15:75132440-75132590	AG04449	skin:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
41	CTCF	chr15:75132440-75132590	BE2_C	brain:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
42	CTCF	chr15:75132420-75132570	GM12864	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
43	CTCF	chr15:75132460-75132610	HEK293	kidney:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
44	CTCF	chr15:75132480-75132630	AG04449	skin:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
45	CTCF	chr15:75132436-75132648	GM12891	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
46	CTCF	chr15:75132460-75132610	HPAF	blood vessel:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
47	CTCF	chr15:75132440-75132590	GM12865	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
48	CTCF	chr15:75132445-75132656	GM19240	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
49	CTCF	chr15:75132420-75132570	HUVEC	blood vessel:	n/a	chr15:75132535-75132553 chr15:75132537-75132550
50	CTCF	chr15:75132420-75132570	GM12867	blood:	n/a	chr15:75132535-75132553 chr15:75132537-75132550

No.	Distal block	Cell Line	Cell type
1	chr15:75083424..75086045-chr15:75130919..75133658,2	K562	blood:
2	chr15:75115272..75120114-chr15:75130983..75135707,7	K562	blood:
3	chr15:75129767..75136088-chr15:75163908..75167881,8	K562	blood:
4	chr15:75132063..75136088-chr15:75165447..75167881,5	K562	blood:
5	chr15:75106165..75113668-chr15:75132311..75136608,10	MCF-7	breast:
6	chr15:75063457..75064044-chr15:75132063..75132629,2	K562	blood:
7	chr15:75073376..75079113-chr15:75130007..75137097,15	MCF-7	breast:
8	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
9	chr15:75131716..75139878-chr15:75227772..75233177,11	MCF-7	breast:

Variant related genes	Relation type
ULK3	TF binding region
ENSG00000260824	Chromatin interaction
ENSG00000213578	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000178802	Chromatin interaction

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

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

rs_ID	r²[population]
rs12898397	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290572	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs936227	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS 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	46 gene(s)	inside rSNPs	diseases
3	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv904382	chr15:75129594-75140854	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569992	chr15:75132319-75137868	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12908814	SCAMP2	cis	Whole Blood	GTEx
rs12908814	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75121400-75134600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75121800-75134600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:75123800-75134200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:75123800-75134200	Weak transcription	Primary B cells from cord blood	blood
5	chr15:75123800-75134400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:75123800-75134400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:75123800-75134400	Weak transcription	HSMM	muscle
8	chr15:75124000-75134400	Weak transcription	HSMMtube	muscle
9	chr15:75124400-75134400	Weak transcription	Fetal Lung	lung
10	chr15:75124800-75134400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:75124800-75134400	Weak transcription	Psoas Muscle	Psoas
12	chr15:75125000-75134000	Weak transcription	Stomach Mucosa	stomach
13	chr15:75125000-75134600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:75125200-75134800	Weak transcription	Aorta	Aorta
15	chr15:75126200-75132800	Weak transcription	Hela-S3	cervix
16	chr15:75126200-75134400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:75126400-75132800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:75126600-75134200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:75126600-75134400	Weak transcription	GM12878-XiMat	blood
20	chr15:75126800-75134600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:75127200-75133400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:75127600-75133600	Strong transcription	Brain Germinal Matrix	brain
23	chr15:75127800-75132800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr15:75127800-75132800	Strong transcription	Right Ventricle	heart
25	chr15:75127800-75133000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:75127800-75133000	Strong transcription	Fetal Muscle Leg	muscle
27	chr15:75127800-75133000	Strong transcription	Pancreas	Pancrea
28	chr15:75127800-75133400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:75127800-75133800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:75127800-75133800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:75127800-75133800	Strong transcription	Fetal Stomach	stomach
32	chr15:75128000-75132800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:75128000-75132800	Strong transcription	Brain Cingulate Gyrus	brain
34	chr15:75128000-75133000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:75128000-75133000	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:75128000-75133400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:75128000-75133400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:75128000-75133400	Strong transcription	Brain Anterior Caudate	brain
39	chr15:75128000-75133400	Strong transcription	Gastric	stomach
40	chr15:75128000-75133400	Strong transcription	Lung	lung
41	chr15:75128000-75133400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr15:75128000-75133400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:75128000-75133400	Strong transcription	Spleen	Spleen
44	chr15:75128000-75133600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:75128000-75133600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:75128000-75133600	Strong transcription	Placenta	Placenta
47	chr15:75128000-75133800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:75128000-75133800	Strong transcription	Primary T cells from cord blood	blood
49	chr15:75128000-75133800	Strong transcription	Liver	Liver
50	chr15:75128000-75134000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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