Variant report

Variant	rs1706821
Chromosome Location	chr15:45477012-45477013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
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	REST	chr15:45476770-45477016	SK-N-SH	brain:	n/a	chr15:45476981-45476995
2	MXI1	chr15:45476431-45481208	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:45476975-45477025	NHBE	bronchial:	n/a
2	chr15:45476975-45477025	HNPCEpiC	eye:	n/a
3	chr15:45476975-45477025	SKMC	muscle:	n/a
4	chr15:45476975-45477025	ECC-1	luminal epithelium:	n/a
5	chr15:45476975-45477025	RPTEC	kidney:	n/a
6	chr15:45476975-45477025	IMR90	lung:	fetal
7	chr15:45476975-45477025	HRCEpiC	kidney:	n/a
8	chr15:45476975-45477025	LNCaP	prostate:	n/a
9	chr15:45476975-45477025	SK-N-SH_RA	brain:	n/a
10	chr15:45476975-45477025	BJ	skin:	n/a
11	chr15:45476975-45477025	HMEC	breast:	n/a
12	chr15:45476975-45477025	SK-N-MC	brain:	n/a
13	chr15:45476975-45477025	HUVEC	blood vessel:	n/a
14	chr15:45476975-45477025	Jurkat	blood:	n/a
15	chr15:45476975-45477025	Hepatocyte	liver:	n/a
16	chr15:45476975-45477025	SK-N-SH	brain:	n/a
17	chr15:45476975-45477025	AG10803	skin:	n/a
18	chr15:45476975-45477025	AG04450	lung:	fetal
19	chr15:45476975-45477025	Caco-2	colon:	n/a
20	chr15:45476975-45477025	PFSK-1	brain:	n/a
21	chr15:45476975-45477025	HCF	heart:	n/a
22	chr15:45476975-45477025	HCT-116	colon:	n/a
23	chr15:45476975-45477025	HCPEpiC	choroid plexus:	n/a
24	chr15:45476975-45477025	NH-A	brain:	n/a
25	chr15:45476975-45477025	HPAEpiC	pulmonary alveolar:	n/a
26	chr15:45476975-45477025	H1-hESC	embryonic stem cell:	embryo
27	chr15:45476975-45477025	HRE	kidney:	n/a
28	chr15:45476975-45477025	GM19239	blood:	n/a
29	chr15:45476975-45477025	HEK293	kidney:	embryo
30	chr15:45476975-45477025	HCM	heart:	n/a
31	chr15:45476975-45477025	HEEpiC	esophagus:	n/a
32	chr15:45476975-45477025	ovcar-3	ovarian:	n/a
33	chr15:45476975-45477025	SAEC	small airway:	n/a
34	chr15:45476975-45477025	Hela-S3	cervix:	n/a
35	chr15:45476975-45477025	GM06990	blood:	n/a
36	chr15:45476975-45477025	A549	lung:	n/a
37	chr15:45476975-45477025	HL-60	blood:	n/a
38	chr15:45476975-45477025	GM12892	blood:	n/a
39	chr15:45476975-45477025	AG04449	skin:	fetal
40	chr15:45476975-45477025	PANC-1	pancreas:	n/a
41	chr15:45476975-45477025	BE2_C	brain:	n/a
42	chr15:45476975-45477025	HIPEpiC	eye:	n/a
43	chr15:45476975-45477025	K562	blood:	n/a
44	chr15:45476975-45477025	AG09319	gingival:	n/a
45	chr15:45476975-45477025	GM12878	blood:	n/a
46	chr15:45476975-45477025	HepG2	liver:	n/a
47	chr15:45476975-45477025	MCF-7	breast:	n/a
48	chr15:45476975-45477025	T-47D	breast:	n/a
49	chr15:45476975-45477025	AoSMC	blood vessel:	n/a
50	chr15:45476975-45477025	U87	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr15:45456567..45458793-chr15:45475778..45478216,2	MCF-7	breast:
2	chr15:45470539..45473664-chr15:45475059..45478000,3	MCF-7	breast:
3	chr15:45476669..45478224-chr15:45478389..45480036,2	K562	blood:
4	chr15:45458109..45460047-chr15:45475007..45477207,2	MCF-7	breast:
5	chr15:45461602..45463661-chr15:45476012..45479858,4	K562	blood:
6	chr15:45465584..45467197-chr15:45475390..45477446,2	MCF-7	breast:
7	chr15:45475968..45478000-chr15:45488455..45490164,2	K562	blood:

No data

Variant related genes	Relation type
SHF	TF binding region
SHF	CpG island
ENSG00000259519	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000259539	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10467979	0.80[AMR][1000 genomes]
rs11634794	0.86[AMR][1000 genomes]
rs11855466	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12323957	0.80[EUR][1000 genomes]
rs12438755	0.82[EUR][1000 genomes]
rs12899786	0.85[EUR][1000 genomes]
rs12902212	0.80[EUR][1000 genomes]
rs12904079	0.97[EUR][1000 genomes]
rs12905053	0.80[EUR][1000 genomes]
rs13329228	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1648287	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1648289	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1648302	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1648311	0.83[EUR][1000 genomes]
rs1648316	0.81[EUR][1000 genomes]
rs1648319	0.80[EUR][1000 genomes]
rs16940351	0.81[ASN][1000 genomes]
rs1706763	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1706822	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1706834	0.85[AMR][1000 genomes]
rs2292467	0.82[EUR][1000 genomes]
rs2467838	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2554455	0.80[AMR][1000 genomes]
rs2554456	0.80[AMR][1000 genomes]
rs2554457	0.80[AMR][1000 genomes]
rs28524974	0.84[AMR][1000 genomes]
rs28526629	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3959644	0.96[EUR][1000 genomes]
rs4514617	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs58547297	0.81[ASN][1000 genomes]
rs62026661	0.98[EUR][1000 genomes]
rs62026665	0.94[EUR][1000 genomes]
rs62026666	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
6	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1706821	CTD-2651B20.1	cis	Artery Tibial	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45459800-45478000	Weak transcription	Aorta	Aorta
2	chr15:45460000-45477200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr15:45460000-45478600	Weak transcription	Thymus	Thymus
4	chr15:45460200-45478000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr15:45460600-45478000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:45460600-45478200	Weak transcription	Adipose Nuclei	Adipose
7	chr15:45462200-45477200	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:45466000-45478800	Weak transcription	Right Ventricle	heart
9	chr15:45466400-45477600	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:45467600-45477400	Weak transcription	Brain Angular Gyrus	brain
11	chr15:45467800-45477400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:45468000-45477800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:45471400-45477400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr15:45471600-45478000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:45471800-45478000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:45472800-45477400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:45473000-45478200	Weak transcription	NH-A	brain
18	chr15:45473200-45477400	Enhancers	Fetal Brain Male	brain
19	chr15:45473200-45478200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr15:45473200-45480400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr15:45473400-45478200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:45473600-45477800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:45473600-45478600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:45473800-45477400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr15:45473800-45477800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:45473800-45478200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:45473800-45478800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr15:45474000-45478200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr15:45474000-45478600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr15:45474200-45477600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:45475400-45478600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:45475600-45478000	Enhancers	Duodenum Mucosa	Duodenum
33	chr15:45475600-45478000	Weak transcription	Fetal Intestine Large	intestine
34	chr15:45475600-45478400	Genic enhancers	Fetal Stomach	stomach
35	chr15:45475600-45478600	Enhancers	Fetal Muscle Trunk	muscle
36	chr15:45475600-45478800	Weak transcription	Stomach Mucosa	stomach
37	chr15:45475800-45477600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr15:45475800-45479400	Flanking Active TSS	Fetal Brain Female	brain
39	chr15:45476000-45477200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:45476000-45477200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:45476000-45477200	Weak transcription	HSMMtube	muscle
42	chr15:45476000-45477400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:45476000-45477600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:45476000-45478000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr15:45476000-45478000	Enhancers	Liver	Liver
46	chr15:45476000-45478000	Weak transcription	Placenta	Placenta
47	chr15:45476000-45478000	Weak transcription	Right Atrium	heart
48	chr15:45476000-45478200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:45476000-45478200	Weak transcription	Lung	lung
50	chr15:45476000-45478400	Enhancers	Fetal Muscle Leg	muscle

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