Variant report

Variant	rs2620683
Chromosome Location	chr12:57984967-57984968
allele	A/G
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	chr12:57984542-57985308	PANC-1	pancreas:	n/a	n/a
2	HDAC2	chr12:57984648-57985233	HepG2	liver:	n/a	n/a
3	REST	chr12:57984649-57985050	HepG2	liver:	n/a	chr12:57984961-57984974 chr12:57984778-57984791
4	TAF1	chr12:57984692-57985203	HepG2	liver:	n/a	n/a
5	PAX5	chr12:57984652-57985497	GM12878	blood:	n/a	n/a
6	KAP1	chr12:57984453-57985087	U2OS	brain:	n/a	n/a
7	CEBPD	chr12:57984584-57985053	HepG2	liver:	n/a	n/a
8	USF1	chr12:57984745-57985257	A549	lung:	n/a	chr12:57984976-57984985 chr12:57984975-57984984 chr12:57984977-57984986 chr12:57984974-57984985 chr12:57984974-57984987 chr12:57984976-57984985 chr12:57984970-57984991
9	TAF1	chr12:57984699-57985163	GM12891	blood:	n/a	n/a
10	HEY1	chr12:57984584-57985189	K562	blood:	n/a	n/a
11	GABPA	chr12:57984719-57985150	Hela-S3	cervix:	n/a	n/a
12	ATF3	chr12:57984726-57985130	GM12878	blood:	n/a	chr12:57984976-57984996 chr12:57984965-57984985 chr12:57984976-57984985
13	MYC	chr12:57984816-57985128	NB4	blood:	n/a	chr12:57984974-57984987 chr12:57984976-57984985 chr12:57984976-57984985 chr12:57984976-57984985
14	CHD2	chr12:57984424-57985175	H1-hESC	embryonic stem cell:	n/a	n/a
15	FOXA1	chr12:57984713-57985070	T-47D	breast:	n/a	n/a
16	POLR2A	chr12:57984651-57985296	PFSK-1	brain:	n/a	n/a
17	SIN3AK20	chr12:57984703-57985667	K562	blood:	n/a	n/a
18	MAX	chr12:57984433-57985290	MCF-7	breast:	n/a	chr12:57984974-57984987 chr12:57984976-57984985 chr12:57984976-57984985 chr12:57984976-57984985
19	GTF2F1	chr12:57984679-57985056	K562	blood:	n/a	n/a
20	ELF1	chr12:57984592-57985296	A549	lung:	n/a	chr12:57985004-57985015 chr12:57985003-57985016 chr12:57985004-57985015 chr12:57985031-57985043 chr12:57984964-57984976 chr12:57985004-57985013
21	YY1	chr12:57984709-57985209	GM12891	blood:	n/a	chr12:57984765-57984779
22	POLR2A	chr12:57984701-57985208	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:57984613-57985671	MCF-7	breast:	n/a	n/a
24	EP300	chr12:57984841-57985140	GM12878	blood:	n/a	n/a
25	IRF1	chr12:57984441-57985184	K562	blood:	n/a	n/a
26	USF1	chr12:57984587-57985430	HCT-116	colon:	n/a	chr12:57984976-57984985 chr12:57984975-57984984 chr12:57984977-57984986 chr12:57984974-57984985 chr12:57984974-57984987 chr12:57984976-57984985 chr12:57984970-57984991
27	USF1	chr12:57984799-57985186	HepG2	liver:	n/a	chr12:57984976-57984985 chr12:57984975-57984984 chr12:57984977-57984986 chr12:57984974-57984985 chr12:57984974-57984987 chr12:57984976-57984985 chr12:57984970-57984991
28	ATF2	chr12:57984864-57985144	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:57984690-57985170	K562	blood:	n/a	n/a
30	RFX5	chr12:57984963-57985021	K562	blood:	n/a	n/a
31	RCOR1	chr12:57984726-57985076	K562	blood:	n/a	n/a
32	SIN3AK20	chr12:57984915-57985294	PANC-1	pancreas:	n/a	n/a
33	YY1	chr12:57984620-57985271	GM12878	blood:	n/a	chr12:57984765-57984779
34	MAFK	chr12:57984688-57985034	Hela-S3	cervix:	n/a	n/a
35	SIN3AK20	chr12:57984598-57985531	H1-hESC	embryonic stem cell:	n/a	n/a
36	USF1	chr12:57984715-57985363	SK-N-SH_RA	brain:	n/a	chr12:57984976-57984985 chr12:57984975-57984984 chr12:57984977-57984986 chr12:57984974-57984985 chr12:57984974-57984987 chr12:57984976-57984985 chr12:57984970-57984991
37	USF2	chr12:57984783-57985186	Hela-S3	cervix:	n/a	chr12:57984976-57984985 chr12:57984975-57984984 chr12:57984977-57984986 chr12:57984974-57984987 chr12:57984976-57984985 chr12:57984974-57984985 chr12:57984970-57984991
38	HMGN3	chr12:57984742-57985399	K562	blood:	n/a	n/a
39	USF1	chr12:57984439-57985726	ECC-1	luminal epithelium:	n/a	chr12:57984976-57984985 chr12:57984975-57984984 chr12:57984977-57984986 chr12:57984974-57984985 chr12:57984974-57984987 chr12:57984976-57984985 chr12:57984970-57984991
40	SIN3A	chr12:57984471-57985733	H1-hESC	embryonic stem cell:	n/a	chr12:57984975-57984984
41	CHD2	chr12:57984537-57985130	K562	blood:	n/a	n/a
42	TAF1	chr12:57984433-57985332	ECC-1	luminal epithelium:	n/a	n/a
43	TBP	chr12:57984611-57985234	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr12:57984649-57985246	K562	blood:	n/a	n/a
45	POLR2A	chr12:57984642-57985272	GM18505	blood:	n/a	n/a
46	GABPA	chr12:57984652-57985313	K562	blood:	n/a	n/a
47	POLR2A	chr12:57984655-57985162	HepG2	liver:	n/a	n/a
48	SIN3AK20	chr12:57984643-57985626	PANC-1	pancreas:	n/a	n/a
49	TAF1	chr12:57984857-57985173	GM12892	blood:	n/a	n/a
50	BHLHE40	chr12:57984647-57985591	K562	blood:	n/a	chr12:57984976-57984985 chr12:57984975-57984984 chr12:57984977-57984986 chr12:57984974-57984987 chr12:57984976-57984985 chr12:57984970-57984991

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:57984923-57984973	SK-N-SH	brain:	n/a
2	chr12:57984920-57984970	HL-60	blood:	n/a
3	chr12:57984920-57984970	LNCaP	prostate:	n/a
4	chr12:57984923-57984973	HCT-116	colon:	n/a
5	chr12:57984920-57984970	Caco-2	colon:	n/a
6	chr12:57984923-57984973	ECC-1	luminal epithelium:	n/a
7	chr12:57984920-57984970	AG09309	skin:	n/a
8	chr12:57984920-57984970	HRCEpiC	kidney:	n/a
9	chr12:57984920-57984970	GM12891	blood:	n/a
10	chr12:57984923-57984973	AG04449	skin:	fetal
11	chr12:57984923-57984973	SKMC	muscle:	n/a
12	chr12:57984920-57984970	Hepatocyte	liver:	n/a
13	chr12:57984923-57984973	SK-N-SH_RA	brain:	n/a
14	chr12:57984920-57984970	PFSK-1	brain:	n/a
15	chr12:57984920-57984970	NH-A	brain:	n/a
16	chr12:57984923-57984973	MCF10A-Er-Src	breast:	n/a
17	chr12:57984920-57984970	Jurkat	blood:	n/a
18	chr12:57984923-57984973	SK-N-MC	brain:	n/a
19	chr12:57984920-57984970	HIPEpiC	eye:	n/a
20	chr12:57984923-57984973	AG10803	skin:	n/a
21	chr12:57984920-57984970	BE2_C	brain:	n/a
22	chr12:57984920-57984970	SK-N-SH_RA	brain:	n/a
23	chr12:57984923-57984973	Hepatocyte	liver:	n/a
24	chr12:57984920-57984970	ProgFib	skin:	n/a
25	chr12:57984923-57984973	NB4	blood:	n/a
26	chr12:57984920-57984970	Hela-S3	cervix:	n/a
27	chr12:57984923-57984973	Hela-S3	cervix:	n/a
28	chr12:57984920-57984970	GM12878	blood:	n/a
29	chr12:57984920-57984970	ovcar-3	ovarian:	n/a
30	chr12:57984923-57984973	HPAEpiC	pulmonary alveolar:	n/a
31	chr12:57984923-57984973	NHDF-neo	bronchial:	n/a
32	chr12:57984920-57984970	HepG2	liver:	n/a
33	chr12:57984923-57984973	NT2-D1	testis:	n/a
34	chr12:57984920-57984970	SAEC	small airway:	n/a
35	chr12:57984923-57984973	HNPCEpiC	eye:	n/a
36	chr12:57984923-57984973	RPTEC	kidney:	n/a
37	chr12:57984923-57984973	A549	lung:	n/a
38	chr12:57984920-57984970	NHDF-neo	bronchial:	n/a
39	chr12:57984920-57984970	CMK	blood:	n/a
40	chr12:57984920-57984970	HCPEpiC	choroid plexus:	n/a
41	chr12:57984923-57984973	HCF	heart:	n/a
42	chr12:57984920-57984970	GM12892	blood:	n/a
43	chr12:57984920-57984970	HCM	heart:	n/a
44	chr12:57984923-57984973	SAEC	small airway:	n/a
45	chr12:57984920-57984970	T-47D	breast:	n/a
46	chr12:57984920-57984970	HMEC	breast:	n/a
47	chr12:57984920-57984970	PANC-1	pancreas:	n/a
48	chr12:57984923-57984973	HCM	heart:	n/a
49	chr12:57984920-57984970	A549	lung:	n/a
50	chr12:57984920-57984970	HEK293	kidney:	embryo

No.	Distal block	Cell Line	Cell type
1	chr12:57983190..57986031-chr12:58086563..58089648,3	K562	blood:
2	chr12:57919943..57923943-chr12:57984305..57987540,4	MCF-7	breast:
3	chr12:57914619..57916153-chr12:57984112..57986210,2	K562	blood:
4	chr12:57984280..57986133-chr12:58130711..58132725,2	K562	blood:
5	chr12:57983454..57989400-chr12:57989791..58002327,29	MCF-7	breast:
6	chr12:57912627..57914339-chr12:57984799..57986574,2	MCF-7	breast:
7	chr12:57983103..57986007-chr12:58086180..58089172,2	MCF-7	breast:
8	chr12:57984859..57985397-chr19:55896847..55897561,2	HCT-116	colon:
9	chr12:49658553..49659361-chr12:57984439..57985376,2	Hela-S3	cervix:
10	chr12:57983391..57985108-chr12:58026747..58028430,2	MCF-7	breast:
11	chr12:57984405..57986520-chr12:58117809..58119763,2	MCF-7	breast:
12	chr12:57983953..57986282-chr12:58144732..58146492,2	K562	blood:
13	chr12:57983992..57986489-chr12:58138776..58141177,2	MCF-7	breast:
14	chr12:57983862..57986521-chr12:58113615..58115210,2	MCF-7	breast:
15	chr12:57983573..57987941-chr12:58024849..58028209,5	MCF-7	breast:
16	chr12:57916409..57919050-chr12:57983099..57985919,3	MCF-7	breast:
17	chr12:57940234..57941945-chr12:57983939..57986632,2	MCF-7	breast:
18	chr12:57939429..57943777-chr12:57984797..57987088,3	K562	blood:
19	chr1:211431871..211432822-chr12:57984812..57985355,2	Hela-S3	cervix:
20	chr12:57984385..57986376-chr12:58138351..58140314,2	K562	blood:
21	chr12:57983656..57985947-chr12:58119170..58122047,3	MCF-7	breast:
22	chr12:57942322..57945252-chr12:57983891..57986391,2	MCF-7	breast:
23	chr12:57869564..57871597-chr12:57983396..57986014,2	K562	blood:
24	chr12:57983700..57986584-chr12:58162901..58165594,2	K562	blood:

Variant related genes	Relation type
PIP4K2C	TF binding region
PIP4K2C	CpG island
ENSG00000175197	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000155980	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000135454	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000117625	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000123329	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1284185	0.84[EUR][1000 genomes]
rs1630692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678508	0.97[EUR][1000 genomes]
rs2600003	0.82[EUR][1000 genomes]
rs2620678	0.89[EUR][1000 genomes]
rs775242	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer 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	96 gene(s)	inside rSNPs	diseases
2	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking 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	96 gene(s)	inside rSNPs	diseases
3	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
6	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers 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	126 gene(s)	inside rSNPs	diseases
8	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv725	chr12:57966549-57993808	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57984000-57986400	Flanking Active TSS	Dnd41	blood
2	chr12:57984200-57985000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:57984200-57985600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:57984200-57985600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr12:57984200-57985600	Active TSS	A549	lung
6	chr12:57984200-57985800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr12:57984200-57985800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:57984200-57985800	Active TSS	Rectal Smooth Muscle	rectum
9	chr12:57984200-57986000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:57984200-57986200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:57984200-57986200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr12:57984200-57986200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:57984200-57986200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:57984200-57986400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr12:57984400-57985000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr12:57984400-57985000	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr12:57984400-57985000	Flanking Active TSS	HUVEC	blood vessel
18	chr12:57984400-57985200	Active TSS	Fetal Muscle Trunk	muscle
19	chr12:57984400-57985400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:57984400-57985400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:57984400-57985600	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr12:57984400-57985600	Active TSS	Placenta Amnion	Placenta Amnion
23	chr12:57984400-57985800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr12:57984400-57985800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:57984400-57985800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:57984400-57985800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:57984400-57985800	Active TSS	Aorta	Aorta
28	chr12:57984400-57985800	Active TSS	HSMMtube	muscle
29	chr12:57984400-57986000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:57984400-57986000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr12:57984600-57985200	Active TSS	H1 Cell Line	embryonic stem cell
32	chr12:57984600-57985200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:57984600-57985200	Active TSS	Lung	lung
34	chr12:57984600-57985400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:57984600-57985400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:57984600-57985400	Active TSS	HSMM	muscle
37	chr12:57984600-57985600	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr12:57984600-57985600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr12:57984600-57985600	Active TSS	Brain Angular Gyrus	brain
40	chr12:57984600-57985600	Active TSS	Psoas Muscle	Psoas
41	chr12:57984600-57985600	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr12:57984600-57985800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:57984600-57985800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr12:57984600-57985800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:57984600-57985800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:57984600-57985800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:57984600-57985800	Active TSS	Gastric	stomach
48	chr12:57984600-57985800	Active TSS	Left Ventricle	heart
49	chr12:57984600-57985800	Active TSS	Ovary	ovary
50	chr12:57984600-57985800	Active TSS	Pancreas	Pancrea

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