Variant report

Variant	rs774896
Chromosome Location	chr12:58025813-58025814
allele	C/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	TAF1	chr12:58025793-58027359	H1-neurons	neurons:	n/a	n/a
2	SUZ12	chr12:58025080-58026351	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr12:58025251-58027842	H1-neurons	neurons:	n/a	chr12:58026939-58026949 chr12:58025258-58025267 chr12:58026880-58026893
4	MAZ	chr12:58025740-58027403	K562	blood:	n/a	n/a
5	CTCF	chr12:58025290-58027579	SK-N-SH	brain:	n/a	chr12:58026689-58026702 chr12:58025999-58026012
6	MAX	chr12:58025620-58027674	A549	lung:	n/a	n/a
7	MAX	chr12:58025803-58027347	A549	lung:	n/a	n/a
8	TCF12	chr12:58025724-58027596	A549	lung:	n/a	chr12:58026170-58026178 chr12:58026653-58026663
9	BACH1	chr12:58025589-58026517	H1-hESC	embryonic stem cell:	n/a	n/a
10	EGR1	chr12:58025617-58025877	K562	blood:	n/a	n/a
11	POLR2A	chr12:58025505-58027615	H1-neurons	neurons:	n/a	n/a
12	MXI1	chr12:58025252-58027427	SK-N-SH	brain:	n/a	n/a
13	ZNF143	chr12:58025795-58025998	H1-hESC	embryonic stem cell:	n/a	n/a
14	ZBTB7A	chr12:58025530-58025887	K562	blood:	n/a	n/a
15	EGR1	chr12:58025570-58025904	K562	blood:	n/a	n/a
16	HMGN3	chr12:58025679-58027197	K562	blood:	n/a	n/a
17	CTBP2	chr12:58024726-58027119	H1-hESC	embryonic stem cell:	n/a	n/a
18	CCNT2	chr12:58025660-58027263	K562	blood:	n/a	chr12:58026633-58026642 chr12:58026082-58026091 chr12:58026832-58026841
19	SMARCB1	chr12:58025781-58027201	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:58025419-58027668	H1-neurons	neurons:	n/a	n/a

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	chr12:57916469..57918452-chr12:58024223..58025919,2	K562	blood:
7	chr12:57939451..57941325-chr12:58024374..58027583,3	K562	blood:
8	chr12:57908910..57916403-chr12:58022622..58028885,15	K562	blood:
9	chr12:57997114..58001112-chr12:58025485..58030490,5	MCF-7	breast:

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

Variant related genes	Relation type
B4GALNT1	TF binding region
ENSG00000240771	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000166987	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	0.84[ASN][1000 genomes]
rs12296706	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12304013	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12318458	0.85[ASN][1000 genomes]
rs12320537	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12322482	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2258877	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2619468	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2619469	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2619470	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2640607	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34919374	0.83[ASN][1000 genomes]
rs35831868	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3899676	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71432310	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs715930	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774897	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774898	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774899	1.00[AMR][1000 genomes];0.99[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	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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58020600-58026200	Weak transcription	Aorta	Aorta
2	chr12:58025000-58026000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr12:58025000-58027600	Active TSS	Brain Angular Gyrus	brain
4	chr12:58025200-58026000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:58025400-58026000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr12:58025400-58026000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:58025400-58026000	Bivalent Enhancer	Placenta	Placenta
8	chr12:58025400-58026200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:58025400-58026200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:58025400-58026200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
11	chr12:58025400-58026400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr12:58025400-58026400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:58025400-58026400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
14	chr12:58025400-58027000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr12:58025400-58027400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr12:58025400-58027400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:58025400-58027600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:58025400-58027600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr12:58025600-58026000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:58025600-58026000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
21	chr12:58025600-58026000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
22	chr12:58025600-58026000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:58025600-58026000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:58025600-58026000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
25	chr12:58025600-58026000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
26	chr12:58025600-58026000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
27	chr12:58025600-58026000	Bivalent Enhancer	Lung	lung
28	chr12:58025600-58026000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
29	chr12:58025600-58026200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:58025600-58026200	Enhancers	Gastric	stomach
31	chr12:58025600-58026200	Enhancers	Pancreas	Pancrea
32	chr12:58025600-58026200	Bivalent/Poised TSS	NHLF	lung
33	chr12:58025600-58026400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:58025600-58026400	Bivalent Enhancer	Fetal Heart	heart
35	chr12:58025600-58026400	Bivalent Enhancer	Fetal Lung	lung
36	chr12:58025600-58026400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
37	chr12:58025600-58026400	Flanking Active TSS	HMEC	breast
38	chr12:58025600-58026600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
39	chr12:58025600-58026600	Active TSS	Fetal Brain Female	brain
40	chr12:58025600-58027000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr12:58025600-58027000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:58025600-58027000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
43	chr12:58025600-58027000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr12:58025600-58027000	Active TSS	Right Atrium	heart
45	chr12:58025600-58027200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr12:58025600-58027200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:58025600-58027200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:58025600-58027200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:58025600-58027200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
50	chr12:58025600-58027400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

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