Variant report

Variant	rs2859580
Chromosome Location	chr3:50194644-50194645
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	chr3:50194548-50194819	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF143	chr3:50194625-50194950	H1-hESC	embryonic stem cell:	n/a	chr3:50194718-50194728
3	POLR2A	chr3:50194535-50194851	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:50194627-50194735	A549	lung:	n/a	n/a
5	POLR2A	chr3:50193788-50195049	PANC-1	pancreas:	n/a	n/a
6	GABPA	chr3:50194559-50194907	H1-hESC	embryonic stem cell:	n/a	n/a
7	REST	chr3:50193898-50195050	H1-neurons	neurons:	n/a	chr3:50194148-50194166 chr3:50194893-50194911 chr3:50194247-50194267
8	ZNF263	chr3:50194530-50194999	HEK293-T-REx	kidney:	n/a	n/a
9	POLR2A	chr3:50194593-50194785	A549	lung:	n/a	n/a
10	MAZ	chr3:50194595-50195001	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:50194193-50194952	HUVEC	blood vessel:	n/a	n/a
12	SIN3A	chr3:50194384-50195041	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYC	chr3:50194642-50194685	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:50194458-50194948	ProgFib	skin:	n/a	n/a
15	YY1	chr3:50194410-50195028	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:50192970-50195122	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr3:50193127-50194992	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr3:50194473-50194883	A549	lung:	n/a	n/a
19	POLR2A	chr3:50192198-50195021	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr3:50193711-50194966	MCF-7	breast:	n/a	n/a
21	POLR2A	chr3:50194404-50194985	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr3:50194502-50194825	ECC-1	luminal epithelium:	n/a	n/a
23	CTBP2	chr3:50194496-50195013	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:50194469-50194970	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr3:50194034-50195101	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr3:50194324-50194801	K562	blood:	n/a	n/a
27	POLR2A	chr3:50194165-50194851	Hela-S3	cervix:	n/a	n/a
28	TBP	chr3:50194642-50194893	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAZ	chr3:50194617-50194966	K562	blood:	n/a	n/a
30	RAD21	chr3:50194586-50194985	H1-hESC	embryonic stem cell:	n/a	chr3:50194871-50194883 chr3:50194871-50194881
31	POLR2A	chr3:50194439-50194945	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr3:50194602-50194795	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr3:50194223-50194957	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr3:50194077-50194991	IMR90	lung:	n/a	n/a
35	POLR2A	chr3:50194494-50194764	A549	lung:	n/a	n/a
36	POLR2A	chr3:50193991-50194992	MCF-7	breast:	n/a	n/a
37	MAZ	chr3:50191779-50196044	IMR90	lung:	n/a	chr3:50194117-50194127 chr3:50193018-50193028 chr3:50195301-50195311 chr3:50195294-50195304 chr3:50193111-50193121
38	SP4	chr3:50194540-50194986	H1-hESC	embryonic stem cell:	n/a	n/a
39	YY1	chr3:50194562-50194878	H1-hESC	embryonic stem cell:	n/a	n/a
40	EGR1	chr3:50194531-50194969	H1-hESC	embryonic stem cell:	n/a	chr3:50194588-50194601 chr3:50194614-50194621
41	POLR2A	chr3:50193999-50194972	MCF-7	breast:	n/a	n/a
42	POLR2A	chr3:50194607-50194719	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr3:50194578-50194802	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr3:50194596-50194946	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50192650..50196663-chr3:50219720..50222472,4	MCF-7	breast:
2	chr3:50149445..50151714-chr3:50193369..50195764,2	MCF-7	breast:
3	chr3:50192501..50194771-chr3:50274192..50275707,2	MCF-7	breast:
4	chr3:50191401..50200098-chr3:50206213..50213809,14	MCF-7	breast:
5	chr3:50194265..50196322-chr3:50231313..50232996,2	MCF-7	breast:
6	chr3:50193794..50194690-chr3:50221433..50222312,2	MCF-7	breast:

Variant related genes	Relation type
SEMA3F	TF binding region
ENSG00000235016	TF binding region
ENSG00000207922	Chromatin interaction
ENSG00000001617	Chromatin interaction
ENSG00000003756	Chromatin interaction
ENSG00000114353	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12631337	0.86[ASN][1000 genomes]
rs2526392	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2526393	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2526395	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2526396	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2526400	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2624836	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2624837	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2624840	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2624842	0.81[ASN][1000 genomes]
rs57842657	0.80[EUR][1000 genomes]
rs6446202	0.85[EUR][1000 genomes]
rs7642692	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
7	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
10	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
13	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
15	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
16	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
17	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
19	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
20	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
22	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
23	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
24	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
25	esv3323037	chr3:50190548-50194846	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50192000-50194800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr3:50192000-50194800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:50192000-50194800	Active TSS	Gastric	stomach
4	chr3:50192000-50194800	Active TSS	Left Ventricle	heart
5	chr3:50192000-50194800	Active TSS	Right Atrium	heart
6	chr3:50192200-50195000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:50192400-50195000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:50192600-50194800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:50192600-50194800	Active TSS	Fetal Kidney	kidney
10	chr3:50193000-50194800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
11	chr3:50193000-50194800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:50193000-50194800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
13	chr3:50193000-50194800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
14	chr3:50193000-50194800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
15	chr3:50193000-50194800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
16	chr3:50193000-50195000	Flanking Bivalent TSS/Enh	Placenta	Placenta
17	chr3:50193200-50194800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:50193200-50194800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:50193200-50195000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:50193200-50195000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:50193200-50195000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr3:50193200-50195000	Flanking Active TSS	A549	lung
23	chr3:50193200-50195000	Flanking Active TSS	HUVEC	blood vessel
24	chr3:50193200-50195400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr3:50193400-50194800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:50193400-50195000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:50193400-50195400	Active TSS	Lung	lung
28	chr3:50193600-50194800	Flanking Active TSS	NHLF	lung
29	chr3:50193600-50194800	Active TSS	Osteobl	bone
30	chr3:50193600-50195000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:50193600-50195200	Flanking Active TSS	HepG2	liver
32	chr3:50193600-50195400	Active TSS	Esophagus	oesophagus
33	chr3:50193600-50196200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:50193600-50197800	Weak transcription	Fetal Heart	heart
35	chr3:50193600-50197800	Weak transcription	Small Intestine	intestine
36	chr3:50193800-50194800	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr3:50193800-50194800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
38	chr3:50193800-50194800	Active TSS	NH-A	brain
39	chr3:50193800-50195400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:50194000-50194800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr3:50194000-50194800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr3:50194000-50194800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:50194000-50194800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr3:50194000-50194800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
45	chr3:50194000-50194800	Active TSS	Placenta Amnion	Placenta Amnion
46	chr3:50194000-50194800	Active TSS	NHDF-Ad	bronchial
47	chr3:50194000-50195000	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:50194200-50194800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:50194200-50195000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr3:50194200-50195000	Flanking Active TSS	Stomach Smooth Muscle	stomach

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