Variant report

Variant	rs12617802
Chromosome Location	chr2:172378009-172378010
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:172377936-172379062	K562	blood:	n/a	chr2:172378829-172378838 chr2:172378822-172378838
2	NR2F2	chr2:172377897-172380493	K562	blood:	n/a	n/a
3	ARID3A	chr2:172377926-172378328	K562	blood:	n/a	n/a
4	GATA2	chr2:172377873-172378300	K562	blood:	n/a	n/a
5	TRIM28	chr2:172377903-172379123	K562	blood:	n/a	n/a
6	CBX3	chr2:172377754-172378178	K562	blood:	n/a	n/a
7	TEAD4	chr2:172377597-172380881	K562	blood:	n/a	n/a
8	MYC	chr2:172377892-172380411	K562	blood:	n/a	n/a
9	GATA1	chr2:172377760-172379435	PBDE	blood:	n/a	n/a
10	POLR2A	chr2:172377948-172378235	K562	blood:	n/a	n/a
11	HCFC1	chr2:172377957-172378058	K562	blood:	n/a	n/a
12	RCOR1	chr2:172377757-172379094	K562	blood:	n/a	n/a
13	TBL1XR1	chr2:172377816-172378062	K562	blood:	n/a	n/a
14	CEBPB	chr2:172378000-172378690	K562	blood:	n/a	n/a
15	TEAD4	chr2:172377897-172379099	K562	blood:	n/a	n/a
16	TBP	chr2:172377950-172380768	K562	blood:	n/a	n/a
17	TAL1	chr2:172377913-172378324	K562	blood:	n/a	n/a
18	RCOR1	chr2:172377915-172379186	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:172377981-172378031	T-47D	breast:	n/a
2	chr2:172377981-172378031	SK-N-SH	brain:	n/a
3	chr2:172377981-172378031	IMR90	lung:	fetal
4	chr2:172377981-172378031	PANC-1	pancreas:	n/a
5	chr2:172377981-172378031	HUVEC	blood vessel:	n/a
6	chr2:172377981-172378031	H1-hESC	embryonic stem cell:	embryo
7	chr2:172377981-172378031	NT2-D1	testis:	n/a
8	chr2:172377981-172378031	HNPCEpiC	eye:	n/a
9	chr2:172377981-172378031	GM06990	blood:	n/a
10	chr2:172377981-172378031	HEEpiC	esophagus:	n/a
11	chr2:172377981-172378031	SK-N-SH_RA	brain:	n/a
12	chr2:172377981-172378031	HepG2	liver:	n/a
13	chr2:172377981-172378031	AG09309	skin:	n/a
14	chr2:172377981-172378031	CMK	blood:	n/a
15	chr2:172377981-172378031	Hela-S3	cervix:	n/a
16	chr2:172377981-172378031	HL-60	blood:	n/a
17	chr2:172377981-172378031	AG10803	skin:	n/a
18	chr2:172377981-172378031	ECC-1	luminal epithelium:	n/a
19	chr2:172377981-172378031	HEK293	kidney:	embryo
20	chr2:172377981-172378031	HRE	kidney:	n/a
21	chr2:172377981-172378031	HRCEpiC	kidney:	n/a
22	chr2:172377981-172378031	NHDF-neo	bronchial:	n/a
23	chr2:172377981-172378031	GM12878	blood:	n/a
24	chr2:172377981-172378031	AG04449	skin:	fetal
25	chr2:172377981-172378031	ProgFib	skin:	n/a
26	chr2:172377981-172378031	HPAEpiC	pulmonary alveolar:	n/a
27	chr2:172377981-172378031	PrEC	prostate:	n/a
28	chr2:172377981-172378031	Caco-2	colon:	n/a
29	chr2:172377981-172378031	HAEpiC	amniotic membrane:	n/a
30	chr2:172377981-172378031	GM12891	blood:	n/a
31	chr2:172377981-172378031	HCM	heart:	n/a
32	chr2:172377981-172378031	NHBE	bronchial:	n/a
33	chr2:172377981-172378031	MCF-7	breast:	n/a
34	chr2:172377981-172378031	NH-A	brain:	n/a
35	chr2:172377981-172378031	SKMC	muscle:	n/a
36	chr2:172377981-172378031	AG09319	gingival:	n/a
37	chr2:172377981-172378031	RPTEC	kidney:	n/a
38	chr2:172377981-172378031	HCT-116	colon:	n/a
39	chr2:172377981-172378031	Jurkat	blood:	n/a
40	chr2:172377981-172378031	A549	lung:	n/a
41	chr2:172377981-172378031	HCF	heart:	n/a
42	chr2:172377981-172378031	U87	brain:	n/a
43	chr2:172377981-172378031	GM19239	blood:	n/a
44	chr2:172377981-172378031	Hepatocyte	liver:	n/a
45	chr2:172377981-172378031	AG04450	lung:	fetal
46	chr2:172377981-172378031	HCPEpiC	choroid plexus:	n/a
47	chr2:172377981-172378031	SAEC	small airway:	n/a
48	chr2:172377981-172378031	ovcar-3	ovarian:	n/a
49	chr2:172377981-172378031	BE2_C	brain:	n/a
50	chr2:172377981-172378031	HIPEpiC	eye:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172288399..172293582-chr2:172376630..172381034,10	K562	blood:
2	chr2:172344598..172348821-chr2:172376554..172380965,4	K562	blood:
3	chr2:172288399..172297381-chr2:172370978..172381493,22	K562	blood:
4	chr2:171784693..171786944-chr2:172376735..172379477,2	K562	blood:
5	chr2:172377500..172380432-chr2:172864656..172866178,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000233762	TF binding region
CYBRD1	TF binding region
ENSG00000233762	CpG island
CYBRD1	CpG island
ENSG00000228507	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11687075	0.85[EUR][1000 genomes]
rs12621138	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692964	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692965	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009270	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs13024499	0.87[EUR][1000 genomes]
rs13401678	0.84[CEU][hapmap]
rs17287442	0.84[CEU][hapmap]
rs17288182	0.85[EUR][1000 genomes]
rs17288294	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs35050777	0.87[EUR][1000 genomes]
rs3806562	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806563	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806564	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806565	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66572658	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66818940	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66975464	0.81[EUR][1000 genomes]
rs6704600	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6726306	0.87[EUR][1000 genomes]
rs67339714	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751899	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6759487	0.86[CEU][hapmap]
rs884409	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646734	0.93[CEU][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	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12617802	CYBRD1	cis	Whole Blood	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172370800-172378400	Weak transcription	Right Ventricle	heart
2	chr2:172373200-172378200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:172373200-172378200	Weak transcription	Osteobl	bone
4	chr2:172373600-172378200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:172373600-172378200	Weak transcription	NH-A	brain
6	chr2:172373600-172378400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:172373600-172378800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:172374400-172378400	Weak transcription	Placenta	Placenta
9	chr2:172376400-172378400	Enhancers	Fetal Muscle Leg	muscle
10	chr2:172376400-172378400	Enhancers	Left Ventricle	heart
11	chr2:172376600-172378400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:172376600-172378400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:172376800-172378200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:172376800-172378200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:172377000-172378200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:172377000-172378400	Enhancers	Fetal Thymus	thymus
17	chr2:172377200-172378200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:172377200-172378200	Weak transcription	Right Atrium	heart
19	chr2:172377200-172378400	Enhancers	Brain Anterior Caudate	brain
20	chr2:172377400-172378200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr2:172377400-172378200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
22	chr2:172377400-172378200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:172377400-172378200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr2:172377400-172378600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:172377600-172378200	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:172377600-172378400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr2:172377600-172378400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:172377600-172378400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:172377800-172378200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr2:172377800-172378200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
31	chr2:172377800-172378200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:172377800-172378400	Enhancers	H9 Cell Line	embryonic stem cell
33	chr2:172377800-172378400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:172377800-172378400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
35	chr2:172377800-172378400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
36	chr2:172377800-172378400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:172377800-172378400	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:172377800-172378400	Enhancers	Duodenum Mucosa	Duodenum
39	chr2:172377800-172378400	Enhancers	Fetal Stomach	stomach
40	chr2:172377800-172378400	Enhancers	NHDF-Ad	bronchial
41	chr2:172377800-172378800	Flanking Active TSS	HSMMtube	muscle
42	chr2:172377800-172378800	Flanking Active TSS	K562	blood
43	chr2:172378000-172378200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:172378000-172378200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:172378000-172378200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr2:172378000-172378200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:172378000-172378200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:172378000-172378200	Enhancers	Adipose Nuclei	Adipose
49	chr2:172378000-172378200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:172378000-172378200	Enhancers	Colon Smooth Muscle	Colon

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