Variant report

Variant	rs12909665
Chromosome Location	chr15:77236574-77236575
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77223524..77226032-chr15:77234679..77237040,2	MCF-7	breast:
2	chr15:77196194..77198493-chr15:77235491..77237833,2	K562	blood:

Variant related genes	Relation type
ENSG00000117906	Chromatin interaction
ENSG00000140386	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12148386	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12438362	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441855	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12595586	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12913810	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12916324	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17380507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17464903	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34338978	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34748201	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35076986	0.95[ASN][1000 genomes]
rs35157989	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35999717	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3829489	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4360890	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886507	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886839	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56234001	0.97[ASN][1000 genomes]
rs58889902	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66508953	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs71398948	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166156	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169663	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8024737	0.91[ASN][1000 genomes]
rs9788684	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12909665	SCAPER	cis	lung	GTEx
rs12909665	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12909665	SCAPER	cis	Artery Tibial	GTEx
rs12909665	SCAPER	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77224800-77243000	Weak transcription	Lung	lung
2	chr15:77224800-77256000	Weak transcription	Pancreas	Pancrea
3	chr15:77225000-77240400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:77225000-77240400	Weak transcription	Spleen	Spleen
5	chr15:77225000-77241000	Weak transcription	Colonic Mucosa	Colon
6	chr15:77225000-77242800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:77225000-77243000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:77225000-77245200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:77225000-77245200	Weak transcription	Esophagus	oesophagus
10	chr15:77225000-77247000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:77225000-77254600	Weak transcription	Aorta	Aorta
12	chr15:77225000-77260200	Weak transcription	Right Ventricle	heart
13	chr15:77225200-77245200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:77225200-77246400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:77225400-77238000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:77225400-77238800	Weak transcription	Stomach Mucosa	stomach
17	chr15:77225400-77255400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:77225600-77243600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:77225800-77243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:77225800-77244600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:77225800-77245000	Weak transcription	Fetal Heart	heart
22	chr15:77226000-77237000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:77226200-77247200	Weak transcription	Fetal Brain Male	brain
24	chr15:77227000-77236800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:77228200-77237200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:77228200-77243000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:77228200-77245600	Weak transcription	HMEC	breast
28	chr15:77229200-77240800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:77229200-77243400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:77229200-77245200	Weak transcription	Small Intestine	intestine
31	chr15:77229200-77251600	Weak transcription	NHLF	lung
32	chr15:77229400-77236800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:77229400-77237400	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:77229400-77237800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:77229400-77239800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:77229400-77240200	Weak transcription	Hela-S3	cervix
37	chr15:77229400-77240600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:77229400-77240800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:77229400-77243000	Weak transcription	Left Ventricle	heart
40	chr15:77229400-77243200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr15:77229400-77249000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:77229400-77254400	Weak transcription	Psoas Muscle	Psoas
43	chr15:77229400-77255000	Weak transcription	Gastric	stomach
44	chr15:77229600-77236600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:77229600-77236600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:77229600-77237400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:77229600-77243600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:77230000-77236600	Weak transcription	Brain Germinal Matrix	brain
49	chr15:77230000-77236800	Weak transcription	HUVEC	blood vessel
50	chr15:77230200-77236600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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