Variant report

Variant	rs884409
Chromosome Location	chr2:172378657-172378658
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr2:172378535-172379214	K562	blood:	n/a	n/a
2	MAZ	chr2:172378512-172380455	K562	blood:	n/a	n/a
3	TAF1	chr2:172378625-172380266	H1-hESC	embryonic stem cell:	n/a	n/a
4	STAT5A	chr2:172378382-172380720	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:172378462-172380386	GM12891	blood:	n/a	n/a
6	BCLAF1	chr2:172378314-172379280	GM12878	blood:	n/a	n/a
7	CTCF	chr2:172378591-172378680	GM13977	blood:	n/a	n/a
8	POLR2A	chr2:172378591-172379460	Gliobla	brain:	n/a	n/a
9	POLR2A	chr2:172378485-172380485	GM18505	blood:	n/a	n/a
10	MAX	chr2:172378437-172380428	A549	lung:	n/a	n/a
11	MAZ	chr2:172378413-172380642	IMR90	lung:	n/a	n/a
12	BHLHE40	chr2:172378595-172378989	GM12878	blood:	n/a	n/a
13	CTCF	chr2:172378600-172378750	AG09309	skin:	n/a	n/a
14	CTCF	chr2:172378580-172378730	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr2:172378560-172378710	AG04449	skin:	n/a	n/a
16	E2F4	chr2:172378628-172378998	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr2:172378481-172379276	HCT-116	colon:	n/a	n/a
18	STAT5A	chr2:172378299-172378935	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:172378580-172379171	SK-N-SH	brain:	n/a	n/a
20	E2F6	chr2:172378427-172380310	K562	blood:	n/a	chr2:172378789-172378800 chr2:172379380-172379392 chr2:172379517-172379527 chr2:172380298-172380305 chr2:172379511-172379520 chr2:172379690-172379699
21	CTCF	chr2:172378520-172378670	AG04450	lung:	n/a	n/a
22	POU2F2	chr2:172378534-172378968	GM12891	blood:	n/a	n/a
23	EBF1	chr2:172378524-172378999	GM12878	blood:	n/a	n/a
24	CTCF	chr2:172378580-172378730	HAc	cerebellar:	n/a	n/a
25	EP300	chr2:172377936-172379062	K562	blood:	n/a	chr2:172378829-172378838 chr2:172378822-172378838
26	POLR2A	chr2:172378424-172380890	HL-60	blood:	n/a	n/a
27	YY1	chr2:172378239-172379265	GM12892	blood:	n/a	chr2:172378827-172378838
28	CHD1	chr2:172378626-172378877	H1-hESC	embryonic stem cell:	n/a	n/a
29	GTF2B	chr2:172378627-172379225	K562	blood:	n/a	n/a
30	CTCF	chr2:172378565-172378855	GM12892	blood:	n/a	n/a
31	CTBP2	chr2:172378602-172380376	H1-hESC	embryonic stem cell:	n/a	n/a
32	GTF2F1	chr2:172378621-172379055	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr2:172378493-172379231	GM12891	blood:	n/a	n/a
34	MYC	chr2:172378590-172379118	K562	blood:	n/a	n/a
35	MAX	chr2:172378532-172380794	NB4	blood:	n/a	n/a
36	POLR2A	chr2:172378344-172379190	IMR90	lung:	n/a	n/a
37	MAX	chr2:172378435-172379125	K562	blood:	n/a	n/a
38	NR2F2	chr2:172377897-172380493	K562	blood:	n/a	n/a
39	CTCF	chr2:172378560-172378710	GM12874	blood:	n/a	n/a
40	CTCF	chr2:172378560-172378710	BJ	skin:	n/a	n/a
41	CTCF	chr2:172378600-172378750	NHDF-neo	bronchial:	n/a	n/a
42	CTCF	chr2:172378560-172378710	HEEpiC	esophagus:	n/a	n/a
43	ATF1	chr2:172378391-172378984	K562	blood:	n/a	n/a
44	ZNF384	chr2:172378630-172379093	K562	blood:	n/a	n/a
45	CTCF	chr2:172378572-172378731	Gliobla	brain:	n/a	n/a
46	CBX3	chr2:172378456-172379076	K562	blood:	n/a	n/a
47	CTCF	chr2:172378600-172378750	HRE	kidney:	n/a	n/a
48	SIN3A	chr2:172378523-172380849	H1-hESC	embryonic stem cell:	n/a	chr2:172379499-172379510 chr2:172379828-172379841 chr2:172379509-172379520
49	CTCF	chr2:172378520-172378670	GM12864	blood:	n/a	n/a
50	NFIC	chr2:172378350-172379409	GM12878	blood:	n/a	n/a

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:

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

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11687075	0.86[EUR][1000 genomes]
rs12617802	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692964	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692965	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009270	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13024499	0.88[EUR][1000 genomes]
rs17287442	0.87[CEU][hapmap]
rs17288182	0.86[EUR][1000 genomes]
rs17288294	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs35050777	0.88[EUR][1000 genomes]
rs3806562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806564	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806565	0.83[CEU][hapmap];0.81[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806566	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66572658	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66818940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66975464	0.82[EUR][1000 genomes]
rs6704600	0.88[EUR][1000 genomes]
rs6726306	0.88[EUR][1000 genomes]
rs67339714	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751899	0.88[EUR][1000 genomes]
rs6759487	0.88[CEU][hapmap]
rs9646734	0.94[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
rs884409	CYBRD1	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172373600-172378800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172377800-172378800	Flanking Active TSS	HSMMtube	muscle
3	chr2:172377800-172378800	Flanking Active TSS	K562	blood
4	chr2:172378000-172378800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr2:172378000-172378800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:172378000-172378800	Enhancers	Fetal Heart	heart
7	chr2:172378000-172378800	Enhancers	Pancreas	Pancrea
8	chr2:172378000-172379000	Enhancers	Stomach Mucosa	stomach
9	chr2:172378200-172378800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr2:172378200-172378800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:172378200-172378800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:172378200-172378800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr2:172378200-172378800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr2:172378200-172378800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr2:172378200-172378800	Flanking Active TSS	A549	lung
16	chr2:172378200-172378800	Flanking Active TSS	HSMM	muscle
17	chr2:172378200-172378800	Flanking Active TSS	NH-A	brain
18	chr2:172378200-172379200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:172378200-172380800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr2:172378200-172381200	Active TSS	Right Atrium	heart
21	chr2:172378400-172378800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
22	chr2:172378400-172378800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:172378400-172378800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:172378400-172378800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr2:172378400-172378800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
26	chr2:172378400-172378800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr2:172378400-172378800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:172378400-172378800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
29	chr2:172378400-172378800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
30	chr2:172378400-172378800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr2:172378400-172378800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:172378400-172378800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr2:172378400-172378800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:172378400-172378800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:172378400-172378800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:172378400-172378800	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr2:172378400-172378800	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr2:172378400-172378800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
39	chr2:172378400-172378800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr2:172378400-172378800	Active TSS	Fetal Muscle Trunk	muscle
41	chr2:172378400-172378800	Flanking Active TSS	Left Ventricle	heart
42	chr2:172378400-172378800	Flanking Active TSS	Psoas Muscle	Psoas
43	chr2:172378400-172378800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr2:172378400-172378800	Flanking Active TSS	NHLF	lung
45	chr2:172378400-172378800	Flanking Active TSS	Osteobl	bone
46	chr2:172378400-172379000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr2:172378400-172379000	Active TSS	Colonic Mucosa	Colon
48	chr2:172378400-172379000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr2:172378400-172379000	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr2:172378400-172379000	Enhancers	Spleen	Spleen

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