Variant report

Variant	rs12939797
Chromosome Location	chr17:15686295-15686296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:15686201-15686306	Lung_OC	lung:	n/a	n/a
2	CTCF	chr17:15686180-15686330	HRE	kidney:	n/a	n/a
3	CTCF	chr17:15686180-15686330	HA-sp	spinal cord:	n/a	n/a
4	CTCF	chr17:15686160-15686310	BJ	skin:	n/a	n/a
5	CTCF	chr17:15686215-15686295	Pancreas_OC	pancreas:	n/a	n/a
6	POLR2A	chr17:15686283-15686356	A549	lung:	n/a	n/a
7	POLR2A	chr17:15686275-15686384	A549	lung:	n/a	n/a
8	CTCF	chr17:15686180-15686330	HCFaa	heart:	n/a	n/a
9	CTCF	chr17:15686160-15686310	HCPEpiC	choroid plexus:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:15686294-15686344	SK-N-SH	brain:	n/a
2	chr17:15686294-15686344	IMR90	lung:	fetal
3	chr17:15686294-15686344	GM19239	blood:	n/a
4	chr17:15686294-15686344	AG09309	skin:	n/a
5	chr17:15686294-15686344	BE2_C	brain:	n/a
6	chr17:15686294-15686344	Caco-2	colon:	n/a
7	chr17:15686294-15686344	HCT-116	colon:	n/a
8	chr17:15686294-15686344	HMEC	breast:	n/a
9	chr17:15686294-15686344	HEEpiC	esophagus:	n/a
10	chr17:15686294-15686344	GM12878	blood:	n/a
11	chr17:15686294-15686344	HUVEC	blood vessel:	n/a
12	chr17:15686294-15686344	H1-hESC	embryonic stem cell:	embryo
13	chr17:15686294-15686344	LNCaP	prostate:	n/a
14	chr17:15686294-15686344	T-47D	breast:	n/a
15	chr17:15686294-15686344	AoSMC	blood vessel:	n/a
16	chr17:15686294-15686344	HCPEpiC	choroid plexus:	n/a
17	chr17:15686294-15686344	U87	brain:	n/a
18	chr17:15686294-15686344	Hela-S3	cervix:	n/a
19	chr17:15686294-15686344	SK-N-SH_RA	brain:	n/a
20	chr17:15686294-15686344	HIPEpiC	eye:	n/a
21	chr17:15686294-15686344	ProgFib	skin:	n/a
22	chr17:15686294-15686344	AG09319	gingival:	n/a
23	chr17:15686294-15686344	ovcar-3	ovarian:	n/a
24	chr17:15686294-15686344	MCF10A-Er-Src	breast:	n/a
25	chr17:15686294-15686344	SK-N-MC	brain:	n/a
26	chr17:15686294-15686344	HEK293	kidney:	embryo
27	chr17:15686294-15686344	HL-60	blood:	n/a
28	chr17:15686294-15686344	HAEpiC	amniotic membrane:	n/a
29	chr17:15686294-15686344	HPAEpiC	pulmonary alveolar:	n/a
30	chr17:15686294-15686344	BJ	skin:	n/a
31	chr17:15686294-15686344	HNPCEpiC	eye:	n/a
32	chr17:15686294-15686344	MCF-7	breast:	n/a
33	chr17:15686294-15686344	GM12891	blood:	n/a
34	chr17:15686294-15686344	NT2-D1	testis:	n/a
35	chr17:15686294-15686344	K562	blood:	n/a
36	chr17:15686294-15686344	NH-A	brain:	n/a
37	chr17:15686294-15686344	GM12892	blood:	n/a
38	chr17:15686294-15686344	PrEC	prostate:	n/a
39	chr17:15686294-15686344	ECC-1	luminal epithelium:	n/a
40	chr17:15686294-15686344	NHBE	bronchial:	n/a
41	chr17:15686294-15686344	HRE	kidney:	n/a
42	chr17:15686294-15686344	GM06990	blood:	n/a
43	chr17:15686294-15686344	RPTEC	kidney:	n/a
44	chr17:15686294-15686344	SKMC	muscle:	n/a
45	chr17:15686294-15686344	AG04450	lung:	fetal
46	chr17:15686294-15686344	HCM	heart:	n/a
47	chr17:15686294-15686344	AG04449	skin:	fetal
48	chr17:15686294-15686344	A549	lung:	n/a
49	chr17:15686294-15686344	NB4	blood:	n/a
50	chr17:15686294-15686344	PFSK-1	brain:	n/a

No data

Variant related genes	Relation type
MEIS3P1	TF binding region
IL6STP1	TF binding region
IL6STP1	CpG island
MEIS3P1	CpG island

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11078315	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34071462	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4792677	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs508959	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66688787	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
4	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv907705	chr17:15611495-15717546	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
8	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
9	nsv1061222	chr17:15672934-15999778	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv11477	chr17:15676903-15688164	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
11	nsv442411	chr17:15677001-15694785	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12939797	CTD-3157E16.1	cis	Artery Tibial	GTEx
rs12939797	MEIS3P1	cis	Artery Tibial	GTEx
rs12939797	CTD-3157E16.1	cis	Adipose Subcutaneous	GTEx
rs12939797	CTD-3157E16.1	cis	Thyroid	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15685600-15686400	Enhancers	Fetal Lung	lung
2	chr17:15685600-15687200	Enhancers	Colon Smooth Muscle	Colon
3	chr17:15685800-15686400	Active TSS	Ovary	ovary
4	chr17:15685800-15686400	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr17:15685800-15686400	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr17:15685800-15686600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:15685800-15686600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:15685800-15686600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr17:15685800-15686800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:15686000-15686400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:15686000-15686400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr17:15686000-15686600	Active TSS	Adipose Nuclei	Adipose
13	chr17:15686000-15686600	Active TSS	Fetal Muscle Trunk	muscle
14	chr17:15686000-15686600	Enhancers	Placenta	Placenta
15	chr17:15686000-15686600	Active TSS	Left Ventricle	heart
16	chr17:15686000-15686600	Active TSS	Right Atrium	heart
17	chr17:15686000-15686800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr17:15686000-15686800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:15686200-15686400	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr17:15686200-15686400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr17:15686200-15686400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr17:15686200-15686400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr17:15686200-15686400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr17:15686200-15686400	Bivalent/Poised TSS	Fetal Stomach	stomach
25	chr17:15686200-15686400	Active TSS	HMEC	breast
26	chr17:15686200-15686400	Bivalent/Poised TSS	NHEK	skin
27	chr17:15686200-15686600	Bivalent/Poised TSS	Primary monocytes fromperipheralblood	blood
28	chr17:15686200-15686600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:15686200-15686600	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr17:15686200-15686600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr17:15686200-15686600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:15686200-15686600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:15686200-15686600	Active TSS	Aorta	Aorta
34	chr17:15686200-15686600	Active TSS	Brain Angular Gyrus	brain
35	chr17:15686200-15686600	Active TSS	Brain Anterior Caudate	brain
36	chr17:15686200-15686600	Active TSS	Brain Germinal Matrix	brain
37	chr17:15686200-15686600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
38	chr17:15686200-15686600	Active TSS	Colonic Mucosa	Colon
39	chr17:15686200-15686600	Active TSS	Duodenum Mucosa	Duodenum
40	chr17:15686200-15686600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr17:15686200-15686600	Active TSS	Esophagus	oesophagus
42	chr17:15686200-15686600	Active TSS	Fetal Brain Female	brain
43	chr17:15686200-15686600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
44	chr17:15686200-15686600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
45	chr17:15686200-15686600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr17:15686200-15686600	Active TSS	Fetal Muscle Leg	muscle
47	chr17:15686200-15686600	Active TSS	Gastric	stomach
48	chr17:15686200-15686600	Active TSS	Lung	lung
49	chr17:15686200-15686600	Active TSS	Pancreas	Pancrea
50	chr17:15686200-15686600	Bivalent/Poised TSS	Psoas Muscle	Psoas

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