Variant report

Variant	rs58678485
Chromosome Location	chr2:86426238-86426239
allele	C/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	POLR2A	chr2:86425990-86427055	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr2:86426150-86426979	SK-N-MC	brain:	n/a	n/a
3	CBX3	chr2:86426234-86427079	HCT-116	colon:	n/a	n/a
4	CBX3	chr2:86426147-86426844	K562	blood:	n/a	n/a
5	POLR2A	chr2:86426027-86427133	PANC-1	pancreas:	n/a	n/a
6	CEBPB	chr2:86426235-86426396	A549	lung:	n/a	n/a
7	POLR2A	chr2:86426216-86426882	PANC-1	pancreas:	n/a	n/a
8	MXI1	chr2:86426148-86427499	SK-N-SH	brain:	n/a	n/a
9	ZNF384	chr2:86425985-86426845	K562	blood:	n/a	n/a
10	SIX5	chr2:86426220-86427249	A549	lung:	n/a	n/a
11	GTF3C2	chr2:86426068-86426806	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr2:86426219-86427029	GM12878	blood:	n/a	n/a
13	MYBL2	chr2:86426103-86427195	HepG2	liver:	n/a	n/a
14	TAF1	chr2:86426143-86427189	A549	lung:	n/a	n/a
15	POLR2A	chr2:86426136-86426968	HUVEC	blood vessel:	n/a	n/a
16	JUND	chr2:86426199-86426863	A549	lung:	n/a	n/a
17	TCF12	chr2:86426219-86426956	ECC-1	luminal epithelium:	n/a	n/a
18	ELF1	chr2:86425955-86426923	GM12878	blood:	n/a	chr2:86426517-86426528
19	YY1	chr2:86426227-86427150	A549	lung:	n/a	chr2:86426609-86426621
20	HCFC1	chr2:86426162-86427730	Hela-S3	cervix:	n/a	n/a
21	BCL3	chr2:86426229-86426915	A549	lung:	n/a	n/a
22	SP1	chr2:86426233-86426936	A549	lung:	n/a	chr2:86426532-86426546 chr2:86426921-86426935 chr2:86426796-86426805
23	POLR2A	chr2:86426146-86426967	U87	brain:	n/a	n/a
24	NR2F2	chr2:86426089-86427257	K562	blood:	n/a	n/a
25	REST	chr2:86426235-86427206	H1-neurons	neurons:	n/a	chr2:86427154-86427164
26	POLR2A	chr2:86426154-86426983	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr2:86426218-86426993	MCF-7	breast:	n/a	n/a
28	POLR2A	chr2:86426167-86427205	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr2:86426163-86426961	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr2:86425265-86427120	HepG2	liver:	n/a	n/a
31	GABPA	chr2:86426216-86427091	MCF-7	breast:	n/a	n/a
32	POLR2A	chr2:86426221-86426911	SK-N-SH	brain:	n/a	n/a
33	TCF12	chr2:86426039-86427298	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86424285..86426477-chr5:133860624..133863238,2	MCF-7	breast:
2	chr2:86420213..86424453-chr2:86424933..86430971,16	MCF-7	breast:
3	chr2:86331612..86333310-chr2:86425160..86426981,2	MCF-7	breast:

Variant related genes	Relation type
IMMT	TF binding region
MRPL35	TF binding region
ENSG00000043143	Chromatin interaction
ENSG00000132305	Chromatin interaction
ENSG00000265420	Chromatin interaction
ENSG00000273080	Chromatin interaction
ENSG00000068654	Chromatin interaction
ENSG00000132300	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2241434	0.83[EUR][1000 genomes]
rs3764948	0.83[EUR][1000 genomes]
rs3770063	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770064	0.88[ASN][1000 genomes]
rs41291149	1.00[AMR][1000 genomes]
rs58002521	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59185549	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59649940	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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 miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv458574	chr2:86385728-86507688	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
21	nsv582372	chr2:86385728-86507688	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86423400-86426400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:86423400-86426400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:86423400-86426400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:86423400-86426400	Weak transcription	Gastric	stomach
5	chr2:86423400-86426400	Weak transcription	Spleen	Spleen
6	chr2:86423400-86426400	Weak transcription	NHDF-Ad	bronchial
7	chr2:86424200-86426600	Weak transcription	Fetal Heart	heart
8	chr2:86425600-86427200	Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr2:86425600-86427200	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr2:86425800-86426400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:86425800-86426400	Enhancers	Fetal Brain Male	brain
12	chr2:86425800-86427000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:86425800-86427200	Active TSS	Brain Hippocampus Middle	brain
14	chr2:86425800-86427200	Active TSS	Colon Smooth Muscle	Colon
15	chr2:86425800-86427200	Active TSS	Fetal Brain Female	brain
16	chr2:86425800-86427400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:86425800-86427400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:86425800-86427400	Active TSS	Stomach Smooth Muscle	stomach
19	chr2:86425800-86427800	Active TSS	NH-A	brain
20	chr2:86425800-86428200	Active TSS	A549	lung
21	chr2:86425800-86429800	Active TSS	GM12878-XiMat	blood
22	chr2:86426000-86426400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr2:86426000-86426400	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr2:86426000-86426400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr2:86426000-86426400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:86426000-86426400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr2:86426000-86426400	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr2:86426000-86426400	Flanking Active TSS	Placenta	Placenta
29	chr2:86426000-86426400	Flanking Active TSS	Fetal Thymus	thymus
30	chr2:86426000-86426600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr2:86426000-86426600	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr2:86426000-86426600	Active TSS	HepG2	liver
33	chr2:86426000-86426800	Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr2:86426000-86426800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr2:86426000-86427000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:86426000-86427000	Active TSS	Primary T cells from cord blood	blood
37	chr2:86426000-86427000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:86426000-86427000	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr2:86426000-86427000	Active TSS	Colonic Mucosa	Colon
40	chr2:86426000-86427000	Active TSS	Duodenum Mucosa	Duodenum
41	chr2:86426000-86427000	Active TSS	Fetal Lung	lung
42	chr2:86426000-86427000	Active TSS	Rectal Smooth Muscle	rectum
43	chr2:86426000-86427200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:86426000-86427200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:86426000-86427200	Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr2:86426000-86427200	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr2:86426000-86427200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:86426000-86427200	Active TSS	Brain Cingulate Gyrus	brain
49	chr2:86426000-86427200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr2:86426000-86427200	Active TSS	Pancreas	Pancrea

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