Variant report

Variant	rs2258877
Chromosome Location	chr12:58026021-58026022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58025843-58027192	K562	blood:	n/a	n/a
2	UBTF	chr12:58025989-58027212	K562	blood:	n/a	n/a
3	TAF1	chr12:58025793-58027359	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr12:58026020-58026037	K562	blood:	n/a	n/a
5	E2F6	chr12:58025823-58027509	A549	lung:	n/a	chr12:58027192-58027201
6	CTCF	chr12:58026020-58026170	AG04449	skin:	n/a	n/a
7	SUZ12	chr12:58025080-58026351	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr12:58025251-58027842	H1-neurons	neurons:	n/a	chr12:58026939-58026949 chr12:58025258-58025267 chr12:58026880-58026893
9	MAZ	chr12:58025740-58027403	K562	blood:	n/a	n/a
10	CTCF	chr12:58025290-58027579	SK-N-SH	brain:	n/a	chr12:58026689-58026702 chr12:58025999-58026012
11	MAX	chr12:58025620-58027674	A549	lung:	n/a	n/a
12	RCOR1	chr12:58026016-58027573	K562	blood:	n/a	n/a
13	MAX	chr12:58025803-58027347	A549	lung:	n/a	n/a
14	TCF12	chr12:58025724-58027596	A549	lung:	n/a	chr12:58026170-58026178 chr12:58026653-58026663
15	BACH1	chr12:58025589-58026517	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr12:58025973-58027178	K562	blood:	n/a	n/a
17	BHLHE40	chr12:58026000-58026564	K562	blood:	n/a	n/a
18	ELF1	chr12:58025914-58026361	GM12878	blood:	n/a	n/a
19	SIN3A	chr12:58025853-58027193	H1-hESC	embryonic stem cell:	n/a	chr12:58026939-58026948
20	POLR2A	chr12:58025505-58027615	H1-neurons	neurons:	n/a	n/a
21	REST	chr12:58025912-58027284	H1-neurons	neurons:	n/a	chr12:58026939-58026949 chr12:58026880-58026893
22	MXI1	chr12:58025252-58027427	SK-N-SH	brain:	n/a	n/a
23	HA-E2F1	chr12:58025936-58027531	MCF-7	breast:	n/a	chr12:58027192-58027201
24	ZNF263	chr12:58025874-58027149	K562	blood:	n/a	n/a
25	E2F6	chr12:58025890-58027512	K562	blood:	n/a	chr12:58027192-58027201
26	NR2F2	chr12:58025966-58026604	K562	blood:	n/a	n/a
27	HMGN3	chr12:58025679-58027197	K562	blood:	n/a	n/a
28	CTCF	chr12:58025980-58026130	SK-N-SH_RA	brain:	n/a	chr12:58025999-58026012
29	CTBP2	chr12:58024726-58027119	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr12:58025888-58027618	A549	lung:	n/a	chr12:58026689-58026702 chr12:58025999-58026012
31	CREB1	chr12:58025921-58026579	A549	lung:	n/a	n/a
32	ZBTB7A	chr12:58025959-58027402	ECC-1	luminal epithelium:	n/a	n/a
33	ZBTB7A	chr12:58025888-58027175	K562	blood:	n/a	n/a
34	CCNT2	chr12:58025660-58027263	K562	blood:	n/a	chr12:58026633-58026642 chr12:58026082-58026091 chr12:58026832-58026841
35	SMARCB1	chr12:58025781-58027201	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr12:58025419-58027668	H1-neurons	neurons:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58026010-58026060	HCM	heart:	n/a
2	chr12:58026010-58026060	Hepatocyte	liver:	n/a
3	chr12:58026010-58026060	HCF	heart:	n/a
4	chr12:58026010-58026060	PANC-1	pancreas:	n/a
5	chr12:58026010-58026060	AG10803	skin:	n/a
6	chr12:58026010-58026060	RPTEC	kidney:	n/a
7	chr12:58026010-58026060	AoSMC	blood vessel:	n/a
8	chr12:58026010-58026060	Hela-S3	cervix:	n/a
9	chr12:58026010-58026060	HRE	kidney:	n/a
10	chr12:58026010-58026060	BE2_C	brain:	n/a
11	chr12:58026010-58026060	HUVEC	blood vessel:	n/a
12	chr12:58026010-58026060	GM12891	blood:	n/a
13	chr12:58026010-58026060	A549	lung:	n/a
14	chr12:58026010-58026060	AG04449	skin:	fetal
15	chr12:58026010-58026060	HCT-116	colon:	n/a
16	chr12:58026010-58026060	PFSK-1	brain:	n/a
17	chr12:58026010-58026060	PrEC	prostate:	n/a
18	chr12:58026010-58026060	HPAEpiC	pulmonary alveolar:	n/a
19	chr12:58026010-58026060	HEK293	kidney:	embryo
20	chr12:58026010-58026060	AG09319	gingival:	n/a
21	chr12:58026010-58026060	BJ	skin:	n/a
22	chr12:58026010-58026060	ovcar-3	ovarian:	n/a
23	chr12:58026010-58026060	AG04450	lung:	fetal
24	chr12:58026010-58026060	HNPCEpiC	eye:	n/a
25	chr12:58026010-58026060	MCF-7	breast:	n/a
26	chr12:58026010-58026060	Caco-2	colon:	n/a
27	chr12:58026010-58026060	NT2-D1	testis:	n/a
28	chr12:58026010-58026060	HAEpiC	amniotic membrane:	n/a
29	chr12:58026010-58026060	Jurkat	blood:	n/a
30	chr12:58026010-58026060	HRCEpiC	kidney:	n/a
31	chr12:58026010-58026060	U87	brain:	n/a
32	chr12:58026010-58026060	ECC-1	luminal epithelium:	n/a
33	chr12:58026010-58026060	MCF10A-Er-Src	breast:	n/a
34	chr12:58026010-58026060	ProgFib	skin:	n/a
35	chr12:58026010-58026060	HCPEpiC	choroid plexus:	n/a
36	chr12:58026010-58026060	NHBE	bronchial:	n/a
37	chr12:58026010-58026060	SK-N-MC	brain:	n/a
38	chr12:58026010-58026060	H1-hESC	embryonic stem cell:	embryo
39	chr12:58026010-58026060	T-47D	breast:	n/a
40	chr12:58026010-58026060	IMR90	lung:	fetal
41	chr12:58026010-58026060	GM06990	blood:	n/a
42	chr12:58026010-58026060	HMEC	breast:	n/a
43	chr12:58026010-58026060	SAEC	small airway:	n/a
44	chr12:58026010-58026060	GM12892	blood:	n/a
45	chr12:58026010-58026060	GM12878	blood:	n/a
46	chr12:58026010-58026060	HRPEpiC	eye:	n/a
47	chr12:58026010-58026060	HL-60	blood:	n/a
48	chr12:58026010-58026060	NB4	blood:	n/a
49	chr12:58026010-58026060	HEEpiC	esophagus:	n/a
50	chr12:58026010-58026060	SK-N-SH_RA	brain:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57940164..57942070-chr12:58025601..58028102,2	MCF-7	breast:
2	chr12:58004618..58008024-chr12:58024930..58028098,5	MCF-7	breast:
3	chr12:57912525..57914628-chr12:58024523..58026539,2	MCF-7	breast:
4	chr12:57908910..57916122-chr12:58022622..58031573,17	K562	blood:
5	chr12:57983573..57987941-chr12:58024849..58028209,5	MCF-7	breast:
6	chr12:57939451..57941325-chr12:58024374..58027583,3	K562	blood:
7	chr12:57908910..57916403-chr12:58022622..58028885,15	K562	blood:
8	chr12:58026019..58028946-chr12:58148453..58151531,3	K562	blood:
9	chr12:57997114..58001112-chr12:58025485..58030490,5	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCTN2-2	chr12:58025698-58026463	NONHSAT028949

No data

Variant related genes	Relation type
B4GALNT1	TF binding region
B4GALNT1	CpG island
ENSG00000135446	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000139266	Chromatin interaction
ENSG00000166908	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11172290	0.85[ASN][1000 genomes]
rs12296706	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12304013	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12318458	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12320537	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12322482	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2619468	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2619469	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2619470	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2640607	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34919374	0.84[ASN][1000 genomes]
rs35831868	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3899676	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71432310	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs715930	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774896	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774897	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774898	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774899	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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
2	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
3	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

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58020600-58026200	Weak transcription	Aorta	Aorta
2	chr12:58025000-58027600	Active TSS	Brain Angular Gyrus	brain
3	chr12:58025400-58026200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:58025400-58026200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:58025400-58026200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
6	chr12:58025400-58026400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr12:58025400-58026400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:58025400-58026400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
9	chr12:58025400-58027000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr12:58025400-58027400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:58025400-58027400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:58025400-58027600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr12:58025400-58027600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr12:58025600-58026200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:58025600-58026200	Enhancers	Gastric	stomach
16	chr12:58025600-58026200	Enhancers	Pancreas	Pancrea
17	chr12:58025600-58026200	Bivalent/Poised TSS	NHLF	lung
18	chr12:58025600-58026400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:58025600-58026400	Bivalent Enhancer	Fetal Heart	heart
20	chr12:58025600-58026400	Bivalent Enhancer	Fetal Lung	lung
21	chr12:58025600-58026400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
22	chr12:58025600-58026400	Flanking Active TSS	HMEC	breast
23	chr12:58025600-58026600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
24	chr12:58025600-58026600	Active TSS	Fetal Brain Female	brain
25	chr12:58025600-58027000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr12:58025600-58027000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:58025600-58027000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
28	chr12:58025600-58027000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
29	chr12:58025600-58027000	Active TSS	Right Atrium	heart
30	chr12:58025600-58027200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr12:58025600-58027200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:58025600-58027200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:58025600-58027200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:58025600-58027200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
35	chr12:58025600-58027400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr12:58025600-58027400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:58025600-58027400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:58025600-58027400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:58025600-58027600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
40	chr12:58025600-58027600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr12:58025600-58027600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:58025600-58027600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:58025800-58026200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:58025800-58026200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
45	chr12:58025800-58026200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:58025800-58026200	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
47	chr12:58025800-58026200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
48	chr12:58025800-58026200	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
49	chr12:58025800-58026200	Flanking Active TSS	Hela-S3	cervix
50	chr12:58025800-58026200	Flanking Active TSS	HepG2	liver

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