Variant report

Variant	rs828884
Chromosome Location	chr2:74374641-74374642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:159)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:159 , 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	RAD21	chr2:74374608-74374814	K562	blood:	n/a	n/a
3	SMARCC1	chr2:74374055-74375582	Hela-S3	cervix:	n/a	n/a
4	MAX	chr2:74374422-74375350	ECC-1	luminal epithelium:	n/a	chr2:74375092-74375102
5	POLR2A	chr2:74373272-74376114	K562	blood:	n/a	n/a
6	ZNF384	chr2:74374512-74375362	K562	blood:	n/a	n/a
7	POLR2A	chr2:74374212-74376798	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr2:74374600-74374750	GM12864	blood:	n/a	n/a
9	YY1	chr2:74374630-74375371	K562	blood:	n/a	chr2:74375088-74375102 chr2:74375091-74375102
10	PML	chr2:74374476-74375523	K562	blood:	n/a	n/a
11	TAF1	chr2:74374563-74375388	K562	blood:	n/a	n/a
12	E2F4	chr2:74374542-74375276	MCF10A-Er-Src	breast:	n/a	n/a
13	MAX	chr2:74374320-74376068	K562	blood:	n/a	chr2:74375092-74375102
14	CTCF	chr2:74374580-74374730	NHEK	skin:	n/a	n/a
15	RCOR1	chr2:74374441-74375624	HepG2	liver:	n/a	n/a
16	MAZ	chr2:74373939-74375833	IMR90	lung:	n/a	chr2:74375092-74375102
17	MYBL2	chr2:74374565-74375781	HepG2	liver:	n/a	n/a
18	HMGN3	chr2:74374518-74375355	K562	blood:	n/a	n/a
19	MYBL2	chr2:74374281-74375843	HepG2	liver:	n/a	n/a
20	RAD21	chr2:74374418-74375433	HCT-116	colon:	n/a	chr2:74375088-74375101 chr2:74375167-74375181 chr2:74375085-74375104 chr2:74375089-74375099 chr2:74375130-74375143 chr2:74375087-74375099
21	POLR2A	chr2:74374634-74375406	HUVEC	blood vessel:	n/a	n/a
22	TCF12	chr2:74374401-74375950	A549	lung:	n/a	n/a
23	REST	chr2:74374440-74375873	H1-neurons	neurons:	n/a	n/a
24	ESRRA	chr2:74373926-74375506	GM12878	blood:	n/a	n/a
25	TAF1	chr2:74374374-74376073	H1-hESC	embryonic stem cell:	n/a	n/a
26	E2F4	chr2:74374404-74375452	K562	blood:	n/a	n/a
27	TCF12	chr2:74374596-74375342	ECC-1	luminal epithelium:	n/a	n/a
28	BRCA1	chr2:74374514-74374646	HepG2	liver:	n/a	n/a
29	POLR2A	chr2:74374480-74375328	Hela-S3	cervix:	n/a	n/a
30	TBP	chr2:74374563-74375761	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAZ	chr2:74374425-74376048	K562	blood:	n/a	chr2:74375092-74375102
32	CTCF	chr2:74374620-74374770	AG10803	skin:	n/a	n/a
33	MAX	chr2:74374556-74375255	Hela-S3	cervix:	n/a	chr2:74375092-74375102
34	PML	chr2:74374615-74375952	GM12878	blood:	n/a	n/a
35	CTCF	chr2:74374580-74374730	AG04450	lung:	n/a	n/a
36	SIN3AK20	chr2:74374478-74375224	H1-hESC	embryonic stem cell:	n/a	n/a
37	RCOR1	chr2:74374550-74375267	Hela-S3	cervix:	n/a	n/a
38	MAX	chr2:74374322-74374785	K562	blood:	n/a	n/a
39	BCL3	chr2:74374133-74376141	A549	lung:	n/a	n/a
40	CTCF	chr2:74374200-74376113	SK-N-SH	brain:	n/a	chr2:74375089-74375102 chr2:74375087-74375105
41	RUNX3	chr2:74374468-74375294	GM12878	blood:	n/a	n/a
42	YY1	chr2:74374632-74376027	H1-hESC	embryonic stem cell:	n/a	chr2:74375088-74375102 chr2:74375091-74375102
43	RFX5	chr2:74374572-74374702	HepG2	liver:	n/a	n/a
44	POLR2A	chr2:74374586-74376127	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr2:74374487-74375116	A549	lung:	n/a	n/a
46	CTCF	chr2:74374600-74374750	HepG2	liver:	n/a	n/a
47	MTA3	chr2:74374178-74377005	GM12878	blood:	n/a	n/a
48	POLR2A	chr2:74374439-74375779	HepG2	liver:	n/a	n/a
49	TBL1XR1	chr2:74374548-74375450	K562	blood:	n/a	n/a
50	MAX	chr2:74374206-74376149	K562	blood:	n/a	chr2:74375092-74375102

No data

(count:24 , 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	chr2:74206459..74210168-chr2:74373577..74376532,3	K562	blood:
4	chr11:63685552..63686203-chr2:74374074..74375012,2	Hela-S3	cervix:
5	chr2:74208160..74210258-chr2:74374135..74376647,3	MCF-7	breast:
6	chr2:74366917..74386173-chr2:74421816..74431613,38	K562	blood:
7	chr17:41438005..41438655-chr2:74374189..74375018,2	Hela-S3	cervix:
8	chr2:74373650..74375455-chr2:74756768..74758705,2	K562	blood:
9	chr2:74210880..74213761-chr2:74373693..74375989,3	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	chr2:74054362..74057947-chr2:74372650..74375089,3	MCF-7	breast:
17	chr2:74360981..74362934-chr2:74373468..74376245,3	MCF-7	breast:
18	chr2:74347130..74350614-chr2:74373490..74375151,4	K562	blood:
19	chr2:74210880..74212548-chr2:74372314..74375193,2	K562	blood:
20	chr2:74372816..74377340-chr2:74403923..74407839,6	MCF-7	breast:
21	chr2:74347177..74347948-chr2:74374539..74375360,2	MCF-7	breast:
22	chr2:74347109..74347870-chr2:74374605..74375136,2	K562	blood:
23	chr2:74345450..74348977-chr2:74371413..74376785,7	MCF-7	breast:
24	chr2:74373650..74375879-chr2:74756768..74758827,3	K562	blood:

No data

Variant related genes	Relation type
BOLA3	TF binding region
BOLA3-AS1	TF binding region
ENSG00000255989	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000115317	Chromatin interaction
ENSG00000114978	Chromatin interaction
ENSG00000235499	Chromatin interaction
ENSG00000257800	Chromatin interaction
ENSG00000237883	Chromatin interaction
ENSG00000217702	Chromatin interaction
ENSG00000115307	Chromatin interaction
ENSG00000188687	Chromatin interaction
ENSG00000124356	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11126426	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1620482	0.92[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1667601	0.92[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1667605	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1667606	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667609	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1723292	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108164	0.81[CEU][hapmap]
rs34611905	0.83[EUR][1000 genomes]
rs35864597	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546893	0.80[ASN][1000 genomes]
rs702462	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs702466	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7340453	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs7559252	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7562297	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828856	0.85[ASN][1000 genomes]
rs828858	0.81[CEU][hapmap]
rs828873	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828876	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828877	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828882	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]
rs828883	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	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828886	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[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];1.00[ASN][1000 genomes]
rs828889	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828903	0.81[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs844168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv525117	chr2:74358901-74374641	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs828884	MTHFD2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74373400-74374800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr2:74373600-74375600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:74373800-74374800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:74373800-74374800	Flanking Active TSS	Fetal Muscle Leg	muscle
5	chr2:74373800-74374800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr2:74373800-74375800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:74373800-74375800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:74374000-74374800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr2:74374000-74374800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:74374000-74374800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr2:74374000-74375000	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr2:74374000-74375800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:74374000-74375800	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr2:74374000-74376200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr2:74374000-74376200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:74374000-74376400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr2:74374200-74374800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr2:74374200-74374800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:74374200-74374800	Flanking Active TSS	Placenta	Placenta
20	chr2:74374200-74375400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:74374200-74375400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:74374200-74375400	Active TSS	A549	lung
23	chr2:74374200-74375400	Active TSS	HSMM	muscle
24	chr2:74374200-74375400	Active TSS	K562	blood
25	chr2:74374200-74375600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr2:74374200-74375600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr2:74374200-74375600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:74374200-74375600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr2:74374200-74375600	Bivalent/Poised TSS	HepG2	liver
30	chr2:74374200-74375800	Active TSS	NHDF-Ad	bronchial
31	chr2:74374200-74376000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr2:74374200-74376000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:74374200-74376000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr2:74374200-74376200	Active TSS	H1 Cell Line	embryonic stem cell
35	chr2:74374200-74376600	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr2:74374400-74374800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr2:74374400-74374800	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr2:74374400-74375200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:74374400-74375200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:74374400-74375200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:74374400-74375200	Active TSS	Muscle Satellite Cultured Cells	--
42	chr2:74374400-74375200	Active TSS	Spleen	Spleen
43	chr2:74374400-74375200	Active TSS	Dnd41	blood
44	chr2:74374400-74375200	Active TSS	GM12878-XiMat	blood
45	chr2:74374400-74375200	Active TSS	Hela-S3	cervix
46	chr2:74374400-74375200	Active TSS	HUVEC	blood vessel
47	chr2:74374400-74375400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:74374400-74375400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:74374400-74375400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:74374400-74375400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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