Variant report

Variant	rs884408
Chromosome Location	chr2:172378432-172378433
allele	A/G
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	STAT5A	chr2:172378382-172380720	GM12878	blood:	n/a	n/a
2	BCLAF1	chr2:172378314-172379280	GM12878	blood:	n/a	n/a
3	MAZ	chr2:172378413-172380642	IMR90	lung:	n/a	n/a
4	STAT5A	chr2:172378299-172378935	GM12878	blood:	n/a	n/a
5	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
6	EP300	chr2:172377936-172379062	K562	blood:	n/a	chr2:172378829-172378838 chr2:172378822-172378838
7	POLR2A	chr2:172378424-172380890	HL-60	blood:	n/a	n/a
8	YY1	chr2:172378239-172379265	GM12892	blood:	n/a	chr2:172378827-172378838
9	POLR2A	chr2:172378344-172379190	IMR90	lung:	n/a	n/a
10	NR2F2	chr2:172377897-172380493	K562	blood:	n/a	n/a
11	ATF1	chr2:172378391-172378984	K562	blood:	n/a	n/a
12	NFIC	chr2:172378350-172379409	GM12878	blood:	n/a	n/a
13	FOXM1	chr2:172378406-172379401	GM12878	blood:	n/a	n/a
14	YY1	chr2:172378156-172379210	GM12878	blood:	n/a	chr2:172378827-172378838
15	MTA3	chr2:172378210-172380753	GM12878	blood:	n/a	n/a
16	TBL1XR1	chr2:172378423-172379098	K562	blood:	n/a	n/a
17	POLR2A	chr2:172378279-172380848	HL-60	blood:	n/a	n/a
18	CHD2	chr2:172378172-172379066	K562	blood:	n/a	n/a
19	POLR2A	chr2:172378347-172380674	GM12892	blood:	n/a	n/a
20	POLR2A	chr2:172378089-172380704	GM12891	blood:	n/a	n/a
21	PML	chr2:172378236-172380387	GM12878	blood:	n/a	chr2:172379866-172379874
22	POLR2A	chr2:172378407-172380386	K562	blood:	n/a	n/a
23	TRIM28	chr2:172377903-172379123	K562	blood:	n/a	n/a
24	YY1	chr2:172378245-172379176	GM12878	blood:	n/a	chr2:172378827-172378838
25	RUNX3	chr2:172378304-172380536	GM12878	blood:	n/a	n/a
26	YY1	chr2:172378275-172378908	H1-hESC	embryonic stem cell:	n/a	chr2:172378827-172378838
27	YY1	chr2:172378276-172379205	GM12891	blood:	n/a	chr2:172378827-172378838
28	TEAD4	chr2:172377597-172380881	K562	blood:	n/a	n/a
29	STAT3	chr2:172378209-172378441	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr2:172378427-172379308	HUVEC	blood vessel:	n/a	n/a
31	JUN	chr2:172378399-172378805	H1-hESC	embryonic stem cell:	n/a	chr2:172378705-172378713
32	MAX	chr2:172378392-172380397	H1-hESC	embryonic stem cell:	n/a	n/a
33	MYC	chr2:172377892-172380411	K562	blood:	n/a	n/a
34	IRF1	chr2:172378064-172379145	K562	blood:	n/a	n/a
35	E2F6	chr2:172378424-172379859	H1-hESC	embryonic stem cell:	n/a	chr2:172378789-172378800 chr2:172379380-172379392 chr2:172379517-172379527 chr2:172379511-172379520 chr2:172379690-172379699
36	POLR2A	chr2:172378431-172380359	GM12892	blood:	n/a	n/a
37	GATA1	chr2:172377760-172379435	PBDE	blood:	n/a	n/a
38	TCF12	chr2:172378378-172379229	A549	lung:	n/a	n/a
39	MXI1	chr2:172378394-172381158	IMR90	lung:	n/a	n/a
40	E2F6	chr2:172378318-172380102	H1-hESC	embryonic stem cell:	n/a	chr2:172378789-172378800 chr2:172379380-172379392 chr2:172379517-172379527 chr2:172379511-172379520 chr2:172379690-172379699
41	RUNX3	chr2:172378277-172380445	GM12878	blood:	n/a	n/a
42	WRNIP1	chr2:172378392-172378794	GM12878	blood:	n/a	n/a
43	POLR2A	chr2:172378283-172380484	K562	blood:	n/a	n/a
44	POLR2A	chr2:172378430-172379216	K562	blood:	n/a	n/a
45	CBX3	chr2:172378257-172379828	K562	blood:	n/a	n/a
46	UBTF	chr2:172378389-172380530	K562	blood:	n/a	n/a
47	UBTF	chr2:172378417-172380651	K562	blood:	n/a	n/a
48	REST	chr2:172378355-172380564	HL-60	blood:	n/a	chr2:172379828-172379841 chr2:172380175-172380188
49	EP300	chr2:172378393-172379112	GM12878	blood:	n/a	chr2:172378829-172378838 chr2:172378822-172378838
50	POLR2A	chr2:172378381-172380379	H1-hESC	embryonic stem cell:	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
ENSG00000233762	TF binding region
CYBRD1	TF binding region
ENSG00000115806	Chromatin interaction
ENSG00000228507	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12476341	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13428567	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2356783	0.81[EUR][1000 genomes]
rs4467241	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62181670	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62183550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6730441	0.82[EUR][1000 genomes]
rs6734372	0.82[EUR][1000 genomes]
rs6741930	0.81[AMR][1000 genomes]
rs6743679	0.82[EUR][1000 genomes]
rs6751911	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7586144	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7586174	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs884408	CYBRD1	Cis_1M	lymphoblastoid	RTeQTL
rs884408	METTL8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:112 , 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	chr2:172377400-172378600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:172377800-172378800	Flanking Active TSS	HSMMtube	muscle
4	chr2:172377800-172378800	Flanking Active TSS	K562	blood
5	chr2:172378000-172378600	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr2:172378000-172378600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr2:172378000-172378800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr2:172378000-172378800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:172378000-172378800	Enhancers	Fetal Heart	heart
10	chr2:172378000-172378800	Enhancers	Pancreas	Pancrea
11	chr2:172378000-172379000	Enhancers	Stomach Mucosa	stomach
12	chr2:172378200-172378600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:172378200-172378600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:172378200-172378600	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:172378200-172378600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
16	chr2:172378200-172378600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:172378200-172378600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:172378200-172378600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr2:172378200-172378600	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr2:172378200-172378600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr2:172378200-172378800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
22	chr2:172378200-172378800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:172378200-172378800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:172378200-172378800	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr2:172378200-172378800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:172378200-172378800	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr2:172378200-172378800	Flanking Active TSS	A549	lung
28	chr2:172378200-172378800	Flanking Active TSS	HSMM	muscle
29	chr2:172378200-172378800	Flanking Active TSS	NH-A	brain
30	chr2:172378200-172379200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:172378200-172380800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr2:172378200-172381200	Active TSS	Right Atrium	heart
33	chr2:172378400-172378600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:172378400-172378600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
35	chr2:172378400-172378600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:172378400-172378600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:172378400-172378600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:172378400-172378600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
39	chr2:172378400-172378600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
40	chr2:172378400-172378600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
41	chr2:172378400-172378600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:172378400-172378600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:172378400-172378600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr2:172378400-172378600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:172378400-172378600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:172378400-172378600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:172378400-172378600	Enhancers	Liver	Liver
48	chr2:172378400-172378600	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr2:172378400-172378600	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr2:172378400-172378600	Flanking Active TSS	Brain Cingulate Gyrus	brain

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