Variant report

Variant	rs10168513
Chromosome Location	chr2:55452375-55452376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr2:55452212-55452431	K562	blood:	n/a	n/a
2	ZNF143	chr2:55452307-55452386	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:55452297-55452442	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr2:55452155-55452428	K562	blood:	n/a	n/a
5	E2F6	chr2:55452278-55452394	K562	blood:	n/a	n/a
6	RAD21	chr2:55452216-55452451	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr2:55452298-55452402	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr2:55452096-55452494	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr2:55452280-55452430	HMF	breast:	n/a	n/a
10	CTCF	chr2:55452280-55452430	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:55452363-55452413	Hepatocyte	liver:	n/a
2	chr2:55452363-55452413	Hela-S3	cervix:	n/a
3	chr2:55452363-55452413	GM12891	blood:	n/a
4	chr2:55452363-55452413	U87	brain:	n/a
5	chr2:55452363-55452413	HRPEpiC	eye:	n/a
6	chr2:55452363-55452413	MCF10A-Er-Src	breast:	n/a
7	chr2:55452363-55452413	ovcar-3	ovarian:	n/a
8	chr2:55452363-55452413	SAEC	small airway:	n/a
9	chr2:55452363-55452413	HEK293	kidney:	embryo
10	chr2:55452363-55452413	AoSMC	blood vessel:	n/a
11	chr2:55452363-55452413	HCPEpiC	choroid plexus:	n/a
12	chr2:55452363-55452413	AG09319	gingival:	n/a
13	chr2:55452363-55452413	PANC-1	pancreas:	n/a
14	chr2:55452363-55452413	HAEpiC	amniotic membrane:	n/a
15	chr2:55452363-55452413	LNCaP	prostate:	n/a
16	chr2:55452363-55452413	SK-N-SH_RA	brain:	n/a
17	chr2:55452363-55452413	PrEC	prostate:	n/a
18	chr2:55452363-55452413	HEEpiC	esophagus:	n/a
19	chr2:55452363-55452413	AG09309	skin:	n/a
20	chr2:55452363-55452413	K562	blood:	n/a
21	chr2:55452363-55452413	HUVEC	blood vessel:	n/a
22	chr2:55452363-55452413	HIPEpiC	eye:	n/a
23	chr2:55452363-55452413	AG04450	lung:	fetal
24	chr2:55452363-55452413	A549	lung:	n/a
25	chr2:55452363-55452413	HRE	kidney:	n/a
26	chr2:55452363-55452413	BE2_C	brain:	n/a
27	chr2:55452363-55452413	NT2-D1	testis:	n/a
28	chr2:55452363-55452413	ECC-1	luminal epithelium:	n/a
29	chr2:55452363-55452413	GM12892	blood:	n/a
30	chr2:55452363-55452413	Jurkat	blood:	n/a
31	chr2:55452363-55452413	HNPCEpiC	eye:	n/a
32	chr2:55452363-55452413	SKMC	muscle:	n/a
33	chr2:55452363-55452413	AG10803	skin:	n/a
34	chr2:55452363-55452413	HPAEpiC	pulmonary alveolar:	n/a
35	chr2:55452363-55452413	AG04449	skin:	fetal
36	chr2:55452363-55452413	CMK	blood:	n/a
37	chr2:55452363-55452413	H1-hESC	embryonic stem cell:	embryo
38	chr2:55452363-55452413	MCF-7	breast:	n/a
39	chr2:55452363-55452413	NB4	blood:	n/a
40	chr2:55452363-55452413	Caco-2	colon:	n/a
41	chr2:55452363-55452413	RPTEC	kidney:	n/a
42	chr2:55452363-55452413	BJ	skin:	n/a
43	chr2:55452363-55452413	ProgFib	skin:	n/a
44	chr2:55452363-55452413	GM12878	blood:	n/a
45	chr2:55452363-55452413	SK-N-SH	brain:	n/a
46	chr2:55452363-55452413	NHDF-neo	bronchial:	n/a
47	chr2:55452363-55452413	GM06990	blood:	n/a
48	chr2:55452363-55452413	HRCEpiC	kidney:	n/a
49	chr2:55452363-55452413	PFSK-1	brain:	n/a
50	chr2:55452363-55452413	GM19239	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr2:55447082..55449248-chr2:55452286..55454032,2	MCF-7	breast:
2	chr2:55277719..55279534-chr2:55451997..55454923,2	K562	blood:
3	chr2:55452223..55454388-chr2:55835681..55838374,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPS27A-2	chr2:55451842-55453044	NONHSAT070769

No data

Variant related genes	Relation type
CLHC1	TF binding region
CLHC1	CpG island
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10167895	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10193886	0.82[YRI][hapmap]
rs10200424	0.82[YRI][hapmap]
rs13420684	0.82[YRI][hapmap]
rs1437393	0.83[ASW][hapmap];0.90[YRI][hapmap]
rs2118284	0.82[ASW][hapmap];0.82[GIH][hapmap];0.82[YRI][hapmap]
rs6545477	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6711753	0.83[ASW][hapmap];0.86[YRI][hapmap]
rs6717482	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap]
rs6727118	0.82[YRI][hapmap]
rs6727131	0.86[YRI][hapmap]
rs6747364	0.86[YRI][hapmap]
rs7600669	1.00[CHB][hapmap]
rs9677948	0.82[ASW][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10168513	TSPYL6	cis	cerebellum	SCAN
rs10168513	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55450600-55452400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:55450800-55452400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55451000-55452400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:55451000-55452400	Enhancers	Left Ventricle	heart
5	chr2:55451000-55452800	Enhancers	Right Ventricle	heart
6	chr2:55451000-55453000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:55451000-55453800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:55451000-55454000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:55451000-55454200	Weak transcription	Primary B cells from cord blood	blood
10	chr2:55451000-55454200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:55451000-55454400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:55451000-55454800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:55451000-55454800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:55451000-55454800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:55451000-55454800	Weak transcription	HUVEC	blood vessel
16	chr2:55451000-55455000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:55451000-55455000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:55451000-55455000	Weak transcription	Fetal Intestine Large	intestine
19	chr2:55451000-55455000	Weak transcription	Right Atrium	heart
20	chr2:55451000-55455000	Weak transcription	Small Intestine	intestine
21	chr2:55451000-55455200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:55451000-55455200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:55451000-55455200	Weak transcription	Liver	Liver
24	chr2:55451000-55455200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:55451000-55455200	Weak transcription	Fetal Thymus	thymus
26	chr2:55451000-55455200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:55451000-55455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:55451000-55457200	Weak transcription	NHDF-Ad	bronchial
29	chr2:55451000-55457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:55451000-55457600	Weak transcription	HMEC	breast
31	chr2:55451000-55457800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:55451000-55457800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:55451000-55458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:55451000-55458000	Weak transcription	Osteobl	bone
35	chr2:55451000-55458400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:55451000-55458400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:55451000-55458400	Weak transcription	Aorta	Aorta
38	chr2:55451000-55458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:55451000-55458400	Weak transcription	Fetal Brain Female	brain
40	chr2:55451000-55458600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:55451000-55458600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:55451000-55458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:55451000-55458800	Weak transcription	Esophagus	oesophagus
44	chr2:55451000-55458800	Weak transcription	Stomach Mucosa	stomach
45	chr2:55451200-55452400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:55451200-55452400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:55451200-55452400	Enhancers	Fetal Muscle Trunk	muscle
48	chr2:55451200-55452800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr2:55451200-55452800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:55451200-55452800	Strong transcription	HepG2	liver

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