Variant report

Variant	rs17837216
Chromosome Location	chr13:51936635-51936636
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:51936527-51936647	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr13:51931455-51939276	K562	blood:	n/a	n/a
3	POLR2A	chr13:51935361-51938111	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:51936619-51936669	NHDF-neo	bronchial:	n/a
2	chr13:51936619-51936669	HUVEC	blood vessel:	n/a
3	chr13:51936619-51936669	RPTEC	kidney:	n/a
4	chr13:51936619-51936669	PANC-1	pancreas:	n/a
5	chr13:51936619-51936669	SAEC	small airway:	n/a
6	chr13:51936619-51936669	GM12891	blood:	n/a
7	chr13:51936619-51936669	Hela-S3	cervix:	n/a
8	chr13:51936619-51936669	HCM	heart:	n/a
9	chr13:51936619-51936669	GM12878	blood:	n/a
10	chr13:51936619-51936669	HRCEpiC	kidney:	n/a
11	chr13:51936619-51936669	NB4	blood:	n/a
12	chr13:51936619-51936669	IMR90	lung:	fetal
13	chr13:51936619-51936669	A549	lung:	n/a
14	chr13:51936619-51936669	PFSK-1	brain:	n/a
15	chr13:51936619-51936669	SK-N-SH	brain:	n/a
16	chr13:51936619-51936669	HL-60	blood:	n/a
17	chr13:51936619-51936669	HRPEpiC	eye:	n/a
18	chr13:51936619-51936669	Jurkat	blood:	n/a
19	chr13:51936619-51936669	AG04450	lung:	fetal
20	chr13:51936619-51936669	CMK	blood:	n/a
21	chr13:51936619-51936669	PrEC	prostate:	n/a
22	chr13:51936619-51936669	HCPEpiC	choroid plexus:	n/a
23	chr13:51936619-51936669	LNCaP	prostate:	n/a
24	chr13:51936619-51936669	HCF	heart:	n/a
25	chr13:51936619-51936669	BE2_C	brain:	n/a
26	chr13:51936619-51936669	SKMC	muscle:	n/a
27	chr13:51936619-51936669	Caco-2	colon:	n/a
28	chr13:51936619-51936669	HepG2	liver:	n/a
29	chr13:51936619-51936669	U87	brain:	n/a
30	chr13:51936619-51936669	HEEpiC	esophagus:	n/a
31	chr13:51936619-51936669	HNPCEpiC	eye:	n/a
32	chr13:51936619-51936669	HCT-116	colon:	n/a
33	chr13:51936619-51936669	MCF10A-Er-Src	breast:	n/a
34	chr13:51936619-51936669	ovcar-3	ovarian:	n/a
35	chr13:51936619-51936669	AG04449	skin:	fetal
36	chr13:51936619-51936669	MCF-7	breast:	n/a
37	chr13:51936619-51936669	GM19239	blood:	n/a
38	chr13:51936619-51936669	AG10803	skin:	n/a
39	chr13:51936619-51936669	AG09319	gingival:	n/a
40	chr13:51936619-51936669	SK-N-MC	brain:	n/a
41	chr13:51936619-51936669	GM06990	blood:	n/a
42	chr13:51936619-51936669	NHBE	bronchial:	n/a
43	chr13:51936619-51936669	NT2-D1	testis:	n/a
44	chr13:51936619-51936669	BJ	skin:	n/a
45	chr13:51936619-51936669	HPAEpiC	pulmonary alveolar:	n/a
46	chr13:51936619-51936669	ECC-1	luminal epithelium:	n/a
47	chr13:51936619-51936669	HEK293	kidney:	embryo
48	chr13:51936619-51936669	AG09309	skin:	n/a
49	chr13:51936619-51936669	HAEpiC	amniotic membrane:	n/a
50	chr13:51936619-51936669	AoSMC	blood vessel:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51933288..51938259-chr13:52024808..52026901,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269965	TF binding region
ENSG00000269965	CpG island
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11148219	0.82[JPT][hapmap]
rs1547710	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17252166	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17252173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17252180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17252193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17252200	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837217	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4941699	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4942995	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4942996	0.82[JPT][hapmap]
rs4942999	0.82[JPT][hapmap]
rs57845363	0.81[ASN][1000 genomes]
rs61749884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61749885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330735	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74087486	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7984158	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7992891	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7995478	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7995885	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8000429	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8000433	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001333	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8002112	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9563049	0.82[JPT][hapmap]
rs9563055	0.82[JPT][hapmap]
rs9568580	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs9568586	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs9568631	0.86[CHB][hapmap]
rs9591402	0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17837216	Hs.123474	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51900400-51938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr13:51906000-51944400	Weak transcription	Spleen	Spleen
3	chr13:51911800-51938600	Weak transcription	Pancreas	Pancrea
4	chr13:51913400-51944600	Weak transcription	Aorta	Aorta
5	chr13:51917600-51943200	Weak transcription	NHLF	lung
6	chr13:51917800-51942400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:51918400-51938600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr13:51918600-51945000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:51919000-51944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:51921400-51938400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr13:51921400-51938800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:51922800-51941200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr13:51924400-51938600	Weak transcription	A549	lung
14	chr13:51927800-51937200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr13:51929600-51938600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr13:51929800-51936800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr13:51930800-51938600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr13:51931600-51938600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr13:51932000-51945800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:51932000-51947400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr13:51932200-51941000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr13:51932400-51938600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:51932400-51938600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr13:51932400-51942400	Weak transcription	Thymus	Thymus
25	chr13:51932400-51944400	Weak transcription	Fetal Stomach	stomach
26	chr13:51932600-51937400	Weak transcription	Fetal Lung	lung
27	chr13:51932600-51938800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr13:51932600-51944400	Weak transcription	Lung	lung
29	chr13:51932800-51938600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:51932800-51938600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:51932800-51938600	Weak transcription	NHEK	skin
32	chr13:51932800-51943000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr13:51933000-51937600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr13:51933000-51938600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:51933000-51938600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:51933200-51938800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr13:51933400-51945400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr13:51933600-51938400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:51933600-51938600	Weak transcription	Ovary	ovary
40	chr13:51933600-51947600	Weak transcription	Brain Substantia Nigra	brain
41	chr13:51933800-51937400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr13:51933800-51938600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:51933800-51939600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr13:51933800-51947400	Weak transcription	Brain Germinal Matrix	brain
45	chr13:51934000-51937600	Strong transcription	HMEC	breast
46	chr13:51934000-51938000	Strong transcription	NH-A	brain
47	chr13:51934000-51938600	Weak transcription	Brain Angular Gyrus	brain
48	chr13:51934000-51938600	Weak transcription	Fetal Muscle Leg	muscle
49	chr13:51934000-51938800	Weak transcription	Brain Anterior Caudate	brain
50	chr13:51934000-51938800	Weak transcription	Hela-S3	cervix

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