Variant report

Variant	rs12901188
Chromosome Location	chr15:77364899-77364900
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:77364890-77364940	T-47D	breast:	n/a
2	chr15:77364890-77364940	HCPEpiC	choroid plexus:	n/a
3	chr15:77364890-77364940	HRPEpiC	eye:	n/a
4	chr15:77364890-77364940	PFSK-1	brain:	n/a
5	chr15:77364890-77364940	HCT-116	colon:	n/a
6	chr15:77364890-77364940	NB4	blood:	n/a
7	chr15:77364890-77364940	AG04450	lung:	fetal
8	chr15:77364890-77364940	LNCaP	prostate:	n/a
9	chr15:77364890-77364940	SKMC	muscle:	n/a
10	chr15:77364890-77364940	HCF	heart:	n/a
11	chr15:77364890-77364940	AG09309	skin:	n/a
12	chr15:77364890-77364940	HPAEpiC	pulmonary alveolar:	n/a
13	chr15:77364890-77364940	AG09319	gingival:	n/a
14	chr15:77364890-77364940	HL-60	blood:	n/a
15	chr15:77364890-77364940	HCM	heart:	n/a
16	chr15:77364890-77364940	HEK293	kidney:	embryo
17	chr15:77364890-77364940	Hela-S3	cervix:	n/a
18	chr15:77364890-77364940	NT2-D1	testis:	n/a
19	chr15:77364890-77364940	GM19239	blood:	n/a
20	chr15:77364890-77364940	GM06990	blood:	n/a
21	chr15:77364890-77364940	Hepatocyte	liver:	n/a
22	chr15:77364890-77364940	SAEC	small airway:	n/a
23	chr15:77364890-77364940	AG04449	skin:	fetal
24	chr15:77364890-77364940	PrEC	prostate:	n/a
25	chr15:77364890-77364940	SK-N-SH	brain:	n/a
26	chr15:77364890-77364940	IMR90	lung:	fetal
27	chr15:77364890-77364940	U87	brain:	n/a
28	chr15:77364890-77364940	HMEC	breast:	n/a
29	chr15:77364890-77364940	HNPCEpiC	eye:	n/a
30	chr15:77364890-77364940	NH-A	brain:	n/a
31	chr15:77364890-77364940	CMK	blood:	n/a
32	chr15:77364890-77364940	AG10803	skin:	n/a
33	chr15:77364890-77364940	SK-N-MC	brain:	n/a
34	chr15:77364890-77364940	A549	lung:	n/a
35	chr15:77364890-77364940	HIPEpiC	eye:	n/a
36	chr15:77364890-77364940	BE2_C	brain:	n/a
37	chr15:77364890-77364940	MCF10A-Er-Src	breast:	n/a
38	chr15:77364890-77364940	NHDF-neo	bronchial:	n/a
39	chr15:77364890-77364940	HepG2	liver:	n/a
40	chr15:77364890-77364940	GM12892	blood:	n/a
41	chr15:77364890-77364940	NHBE	bronchial:	n/a
42	chr15:77364890-77364940	BJ	skin:	n/a
43	chr15:77364890-77364940	K562	blood:	n/a
44	chr15:77364890-77364940	MCF-7	breast:	n/a
45	chr15:77364890-77364940	PANC-1	pancreas:	n/a
46	chr15:77364890-77364940	ECC-1	luminal epithelium:	n/a
47	chr15:77364890-77364940	ovcar-3	ovarian:	n/a
48	chr15:77364890-77364940	Jurkat	blood:	n/a
49	chr15:77364890-77364940	HRE	kidney:	n/a
50	chr15:77364890-77364940	H1-hESC	embryonic stem cell:	embryo

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77334649..77338471-chr15:77361377..77364899,5	K562	blood:

No data

Variant related genes	Relation type
TSPAN3	CpG island
ENSG00000269951	CpG island
ENSG00000259652	Chromatin interaction
ENSG00000260787	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11072641	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11630497	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636613	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636648	0.93[EUR][1000 genomes]
rs11737	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12372961	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12912792	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16968665	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2404233	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2404234	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34443712	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886509	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886847	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55645420	0.83[ASN][1000 genomes]
rs62007219	0.81[EUR][1000 genomes]
rs7166154	0.81[EUR][1000 genomes]
rs7169831	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8032	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs938501	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS 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	12 gene(s)	inside rSNPs	diseases
8	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12901188	RP11-797A18.4	cis	Adipose Subcutaneous	GTEx
rs12901188	RP11-797A18.4	cis	Esophagus Muscularis	GTEx
rs12901188	RP11-797A18.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77363400-77370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:77363600-77367800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:77363600-77374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:77363800-77367000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:77363800-77367600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:77363800-77367800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:77363800-77367800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:77363800-77367800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:77363800-77367800	Weak transcription	Brain Substantia Nigra	brain
10	chr15:77363800-77369000	Weak transcription	Esophagus	oesophagus
11	chr15:77363800-77374400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:77364000-77367800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:77364000-77367800	Weak transcription	Brain Angular Gyrus	brain
14	chr15:77364000-77367800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:77364000-77367800	Weak transcription	Brain Germinal Matrix	brain
16	chr15:77364000-77367800	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:77364000-77368400	Weak transcription	Brain Anterior Caudate	brain
18	chr15:77364000-77368800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:77364000-77368800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:77364000-77370400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:77364000-77375800	Weak transcription	Right Atrium	heart
22	chr15:77364200-77367600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:77364200-77367800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:77364400-77367800	Weak transcription	Adipose Nuclei	Adipose
25	chr15:77364800-77367800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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