Variant report

Variant	rs828882
Chromosome Location	chr2:74375804-74375805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:109)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:109 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:74374650-74376123	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:74373272-74376114	K562	blood:	n/a	n/a
3	POLR2A	chr2:74374212-74376798	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr2:74375796-74376094	K562	blood:	n/a	n/a
5	FOSL2	chr2:74374813-74376199	HepG2	liver:	n/a	chr2:74375046-74375060
6	YY1	chr2:74375684-74376072	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:74374796-74376078	A549	lung:	n/a	n/a
8	KAP1	chr2:74375180-74376119	U2OS	brain:	n/a	n/a
9	ZNF263	chr2:74374872-74375890	HEK293-T-REx	kidney:	n/a	n/a
10	MAX	chr2:74374320-74376068	K562	blood:	n/a	chr2:74375092-74375102
11	POLR2A	chr2:74374743-74376098	GM12878	blood:	n/a	n/a
12	MAZ	chr2:74373939-74375833	IMR90	lung:	n/a	chr2:74375092-74375102
13	MYBL2	chr2:74374281-74375843	HepG2	liver:	n/a	n/a
14	TCF12	chr2:74374401-74375950	A549	lung:	n/a	n/a
15	REST	chr2:74374440-74375873	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr2:74375158-74376256	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:74374709-74376848	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:74375289-74376167	GM12891	blood:	n/a	n/a
19	POLR2A	chr2:74375777-74376006	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr2:74375751-74376033	K562	blood:	n/a	n/a
21	TAF1	chr2:74374374-74376073	H1-hESC	embryonic stem cell:	n/a	n/a
22	BCL3	chr2:74374791-74376254	A549	lung:	n/a	n/a
23	POLR2A	chr2:74374855-74381076	K562	blood:	n/a	n/a
24	MAZ	chr2:74374425-74376048	K562	blood:	n/a	chr2:74375092-74375102
25	CBX3	chr2:74374859-74375976	K562	blood:	n/a	n/a
26	MAX	chr2:74374812-74376255	H1-hESC	embryonic stem cell:	n/a	chr2:74375092-74375102
27	POLR2A	chr2:74375758-74376062	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:74374752-74376044	K562	blood:	n/a	n/a
29	E2F6	chr2:74375749-74376081	K562	blood:	n/a	n/a
30	PML	chr2:74374615-74375952	GM12878	blood:	n/a	n/a
31	BCL3	chr2:74374133-74376141	A549	lung:	n/a	n/a
32	CTCF	chr2:74374200-74376113	SK-N-SH	brain:	n/a	chr2:74375089-74375102 chr2:74375087-74375105
33	TBP	chr2:74374776-74376043	K562	blood:	n/a	n/a
34	YY1	chr2:74374632-74376027	H1-hESC	embryonic stem cell:	n/a	chr2:74375088-74375102 chr2:74375091-74375102
35	POLR2A	chr2:74374586-74376127	HepG2	liver:	n/a	n/a
36	MTA3	chr2:74374178-74377005	GM12878	blood:	n/a	n/a
37	MAX	chr2:74374206-74376149	K562	blood:	n/a	chr2:74375092-74375102
38	CHD2	chr2:74375338-74375876	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr2:74375322-74376148	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr2:74373927-74376037	K562	blood:	n/a	n/a
41	TBL1XR1	chr2:74375736-74375936	K562	blood:	n/a	n/a
42	MYC	chr2:74374179-74376082	K562	blood:	n/a	chr2:74375092-74375102
43	POLR2A	chr2:74373872-74376093	K562	blood:	n/a	n/a
44	POLR2A	chr2:74374517-74375814	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr2:74375701-74376394	SK-N-SH	brain:	n/a	n/a
46	CHD1	chr2:74375746-74375995	H1-hESC	embryonic stem cell:	n/a	n/a
47	MYC	chr2:74374286-74376093	K562	blood:	n/a	chr2:74375092-74375102
48	POLR2A	chr2:74374669-74376256	PFSK-1	brain:	n/a	n/a
49	YY1	chr2:74375401-74376107	K562	blood:	n/a	n/a
50	CREB1	chr2:74374125-74375889	HepG2	liver:	n/a	n/a

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	chr2:74152937..74154574-chr2:74375552..74378135,2	MCF-7	breast:
18	chr2:74372816..74377340-chr2:74403923..74407839,6	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:

No data

Variant related genes	Relation type
BOLA3	TF binding region
ENSG00000217702	Chromatin interaction
ENSG00000115307	Chromatin interaction
ENSG00000115317	Chromatin interaction
ENSG00000114978	Chromatin interaction
ENSG00000188687	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000124356	Chromatin interaction
ENSG00000255198	Chromatin interaction
ENSG00000114956	Chromatin interaction
ENSG00000255989	Chromatin interaction
ENSG00000237883	Chromatin interaction
ENSG00000257800	Chromatin interaction
ENSG00000235499	Chromatin interaction
ENSG00000140988	Chromatin interaction
ENSG00000255513	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

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];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.94[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];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1667605	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1667606	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1667609	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1723292	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108164	0.81[CEU][hapmap]
rs34611905	0.84[EUR][1000 genomes]
rs35864597	0.81[AMR][1000 genomes];0.99[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[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7340453	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs7559252	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7562297	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828856	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs828858	0.81[CEU][hapmap]
rs828873	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828876	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828877	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828883	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	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828885	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828886	0.97[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];0.90[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[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];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs828882	RTKN	cis	parietal	SCAN
rs828882	MTHFD2	cis	lymphoblastoid	seeQTL
rs828882	BOLA3	cis	parietal	SCAN
rs828882	MTHFD2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74374000-74376200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr2:74374000-74376200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:74374000-74376400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr2:74374200-74376000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr2:74374200-74376000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:74374200-74376000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:74374200-74376200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr2:74374200-74376600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:74374400-74376000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr2:74374400-74376400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:74374600-74376000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:74374600-74376000	Active TSS	Brain Substantia Nigra	brain
13	chr2:74374600-74376000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr2:74374600-74376200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:74374600-74376200	Active TSS	Brain Germinal Matrix	brain
16	chr2:74374600-74376200	Active TSS	Fetal Kidney	kidney
17	chr2:74375200-74376000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:74375200-74376000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr2:74375200-74376000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr2:74375200-74376000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr2:74375200-74376000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr2:74375200-74376000	Flanking Active TSS	Dnd41	blood
23	chr2:74375200-74376000	Flanking Active TSS	GM12878-XiMat	blood
24	chr2:74375200-74376000	Flanking Active TSS	HUVEC	blood vessel
25	chr2:74375200-74376200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:74375200-74376200	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr2:74375200-74376800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:74375400-74376000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:74375400-74376000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:74375400-74376000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:74375400-74376000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:74375400-74376000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr2:74375400-74376000	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr2:74375400-74376000	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr2:74375400-74376000	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr2:74375400-74376000	Flanking Active TSS	Fetal Stomach	stomach
37	chr2:74375400-74376000	Flanking Active TSS	Pancreas	Pancrea
38	chr2:74375400-74376000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr2:74375400-74376000	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr2:74375400-74376000	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr2:74375400-74376000	Flanking Active TSS	HSMM	muscle
42	chr2:74375400-74376000	Flanking Active TSS	NHLF	lung
43	chr2:74375400-74376000	Flanking Active TSS	Osteobl	bone
44	chr2:74375400-74376200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:74375400-74376200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:74375400-74376200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr2:74375400-74376200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:74375400-74376200	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr2:74375400-74376200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr2:74375400-74376200	Flanking Active TSS	HMEC	breast

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