Variant report

Variant	rs828883
Chromosome Location	chr2:74375457-74375458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:197)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:197 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:74374622-74375592	U87	brain:	n/a	n/a
2	POLR2A	chr2:74374650-74376123	ECC-1	luminal epithelium:	n/a	n/a
3	SMARCC1	chr2:74374055-74375582	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr2:74373272-74376114	K562	blood:	n/a	n/a
5	POLR2A	chr2:74374212-74376798	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:74374702-74375681	SK-N-SH	brain:	n/a	n/a
7	MAX	chr2:74374827-74375589	A549	lung:	n/a	chr2:74375092-74375102
8	PML	chr2:74374476-74375523	K562	blood:	n/a	n/a
9	FOSL2	chr2:74374813-74376199	HepG2	liver:	n/a	chr2:74375046-74375060
10	CTCF	chr2:74375340-74375490	SAEC	small airway:	n/a	n/a
11	MXI1	chr2:74374817-74375640	K562	blood:	n/a	n/a
12	CTCF	chr2:74375320-74375470	BJ	skin:	n/a	n/a
13	POLR2A	chr2:74374796-74376078	A549	lung:	n/a	n/a
14	KAP1	chr2:74375180-74376119	U2OS	brain:	n/a	n/a
15	CTCF	chr2:74374795-74375469	HepG2	liver:	n/a	chr2:74375089-74375102 chr2:74375087-74375105
16	POLR2A	chr2:74374678-74375492	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr2:74374763-74375634	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:74374853-74375722	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF263	chr2:74374872-74375890	HEK293-T-REx	kidney:	n/a	n/a
20	MAX	chr2:74374320-74376068	K562	blood:	n/a	chr2:74375092-74375102
21	POLR2A	chr2:74374743-74376098	GM12878	blood:	n/a	n/a
22	RCOR1	chr2:74374441-74375624	HepG2	liver:	n/a	n/a
23	MAZ	chr2:74373939-74375833	IMR90	lung:	n/a	chr2:74375092-74375102
24	EP300	chr2:74374704-74375471	SK-N-SH	brain:	n/a	chr2:74375070-74375079
25	POLR2A	chr2:74374764-74375746	GM12878	blood:	n/a	n/a
26	ZBTB7A	chr2:74374810-74375502	ECC-1	luminal epithelium:	n/a	n/a
27	MYBL2	chr2:74374565-74375781	HepG2	liver:	n/a	n/a
28	ARID3A	chr2:74374946-74375487	K562	blood:	n/a	n/a
29	MYBL2	chr2:74374281-74375843	HepG2	liver:	n/a	n/a
30	NFIC	chr2:74374772-74375701	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:74374740-74375748	GM18505	blood:	n/a	n/a
32	TCF12	chr2:74374401-74375950	A549	lung:	n/a	n/a
33	REST	chr2:74374440-74375873	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr2:74375158-74376256	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:74374709-74376848	GM12878	blood:	n/a	n/a
36	ESRRA	chr2:74373926-74375506	GM12878	blood:	n/a	n/a
37	POLR2A	chr2:74375289-74376167	GM12891	blood:	n/a	n/a
38	POLR2A	chr2:74374763-74375528	HUVEC	blood vessel:	n/a	n/a
39	MAX	chr2:74374818-74375580	GM12878	blood:	n/a	chr2:74375092-74375102
40	CREB1	chr2:74374860-74375721	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr2:74374374-74376073	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr2:74374726-74375733	GM12892	blood:	n/a	n/a
43	GTF2F1	chr2:74374983-74375500	H1-hESC	embryonic stem cell:	n/a	n/a
44	BCL3	chr2:74374791-74376254	A549	lung:	n/a	n/a
45	POLR2A	chr2:74374830-74375515	HepG2	liver:	n/a	n/a
46	MBD4	chr2:74374806-74375555	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:74374717-74375709	PANC-1	pancreas:	n/a	n/a
48	TBP	chr2:74374563-74375761	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr2:74374855-74381076	K562	blood:	n/a	n/a
50	MAZ	chr2:74374425-74376048	K562	blood:	n/a	chr2:74375092-74375102

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74055393..74058315-chr2:74373246..74376437,5	K562	blood:
2	chr2:74372636..74376479-chr2:74402961..74407334,5	K562	blood:
3	chr2:74374841..74376472-chr2:74433391..74435276,2	K562	blood:
4	chr2:74206459..74210168-chr2:74373577..74376532,3	K562	blood:
5	chr2:74208160..74210258-chr2:74374135..74376647,3	MCF-7	breast:
6	chr2:74364875..74366698-chr2:74375403..74377505,2	MCF-7	breast:
7	chr2:74366917..74386173-chr2:74421816..74431613,38	K562	blood:
8	chr2:74210880..74213761-chr2:74373693..74375989,3	K562	blood:
9	chr2:74055762..74057828-chr2:74374741..74376324,2	K562	blood:
10	chr2:74209442..74213118-chr2:74372270..74377274,6	MCF-7	breast:
11	chr2:74210601..74212361-chr2:74374459..74376721,2	MCF-7	breast:
12	chr2:74346321..74348591-chr2:74373615..74376560,4	MCF-7	breast:
13	chr2:74373512..74376720-chr2:74404630..74408955,6	K562	blood:
14	chr2:74367938..74377304-chr2:74421816..74428438,25	K562	blood:
15	chr2:74373555..74376913-chr2:74449791..74454753,5	K562	blood:
16	chr2:74360981..74362934-chr2:74373468..74376245,3	MCF-7	breast:
17	chr2:74372816..74377340-chr2:74403923..74407839,6	MCF-7	breast:
18	chr2:74346117..74347922-chr2:74374665..74375603,8	MCF-7	breast:
19	chr2:74345450..74348977-chr2:74371413..74376785,7	MCF-7	breast:
20	chr2:74373650..74375879-chr2:74756768..74758827,3	K562	blood:
21	chr16:2013639..2015347-chr2:74374765..74376593,2	MCF-7	breast:

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC073263.1-1	chr2:74375278-74375605	XLOC_001532
2	lnc-AC073263.1-1	chr2:74375213-74375605	XLOC_001532
3	lnc-AC073263.1-1	chr2:74375166-74375605	ENSG00000225439.2
4	lnc-AC073263.1-1	chr2:74375136-74375605	ENSG00000225439.2
5	lnc-AC073263.1-2	chr2:74375108-74375605	NONHSAT071665
6	lnc-AC073263.1-2	chr2:74375227-74375605	NONHSAT071668
7	lnc-AC073263.1-2	chr2:74375108-74375605	NR_045634
8	lnc-AC073263.1-1	chr2:74375278-74375605	XLOC_001532

No data

Variant related genes	Relation type
BOLA3	TF binding region
ENSG00000235499	Chromatin interaction
ENSG00000255989	Chromatin interaction
ENSG00000255198	Chromatin interaction
ENSG00000257800	Chromatin interaction
ENSG00000140988	Chromatin interaction
ENSG00000115317	Chromatin interaction
ENSG00000255513	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000237883	Chromatin interaction
ENSG00000188687	Chromatin interaction
ENSG00000115307	Chromatin interaction
ENSG00000217702	Chromatin interaction
ENSG00000124356	Chromatin interaction
ENSG00000114978	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11126426	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1620482	0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1667601	0.92[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1667605	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1667606	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1667609	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1723292	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108164	0.81[CEU][hapmap]
rs34611905	0.84[EUR][1000 genomes]
rs35864597	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546893	0.82[ASN][1000 genomes]
rs702462	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs702466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7340453	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs7559252	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7562297	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828856	0.87[ASN][1000 genomes]
rs828858	0.81[CEU][hapmap]
rs828873	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828876	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828877	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828885	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828886	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828889	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828903	0.81[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs844168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs828883	MTHFD2	cis	multi-tissue	Pritchard
rs828883	MTHFD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74373600-74375600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr2:74373800-74375800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:74373800-74375800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr2:74374000-74375800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:74374000-74375800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr2:74374000-74376200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr2:74374000-74376200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:74374000-74376400	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr2:74374200-74375600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:74374200-74375600	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr2:74374200-74375600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:74374200-74375600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr2:74374200-74375600	Bivalent/Poised TSS	HepG2	liver
14	chr2:74374200-74375800	Active TSS	NHDF-Ad	bronchial
15	chr2:74374200-74376000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr2:74374200-74376000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:74374200-74376000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr2:74374200-74376200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr2:74374200-74376600	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr2:74374400-74375600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:74374400-74375600	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr2:74374400-74375600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:74374400-74375600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:74374400-74375600	Active TSS	Colon Smooth Muscle	Colon
25	chr2:74374400-74375600	Active TSS	Esophagus	oesophagus
26	chr2:74374400-74375600	Active TSS	Left Ventricle	heart
27	chr2:74374400-74375600	Active TSS	Small Intestine	intestine
28	chr2:74374400-74375800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:74374400-74375800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:74374400-74375800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:74374400-74375800	Active TSS	Gastric	stomach
32	chr2:74374400-74375800	Active TSS	Psoas Muscle	Psoas
33	chr2:74374400-74376000	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr2:74374400-74376400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:74374600-74375600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:74374600-74375600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:74374600-74375600	Active TSS	Aorta	Aorta
38	chr2:74374600-74375600	Active TSS	Brain Cingulate Gyrus	brain
39	chr2:74374600-74375600	Active TSS	Fetal Brain Male	brain
40	chr2:74374600-74375600	Active TSS	Fetal Intestine Small	intestine
41	chr2:74374600-74375600	Active TSS	Fetal Lung	lung
42	chr2:74374600-74375600	Active TSS	Ovary	ovary
43	chr2:74374600-74375800	Active TSS	Brain Angular Gyrus	brain
44	chr2:74374600-74375800	Active TSS	Brain Hippocampus Middle	brain
45	chr2:74374600-74375800	Transcr. at gene 5' and 3'	Right Atrium	heart
46	chr2:74374600-74376000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:74374600-74376000	Active TSS	Brain Substantia Nigra	brain
48	chr2:74374600-74376000	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr2:74374600-74376200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:74374600-74376200	Active TSS	Brain Germinal Matrix	brain

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