Variant report

Variant	rs3858674
Chromosome Location	chr12:63327539-63327540
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	ZEB1	chr12:63326895-63329453	HepG2	liver:	n/a	chr12:63329095-63329107 chr12:63329096-63329107
2	MAX	chr12:63327017-63329477	A549	lung:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
3	HA-E2F1	chr12:63326823-63329443	MCF-7	breast:	n/a	chr12:63327280-63327287 chr12:63328820-63328835 chr12:63328824-63328836 chr12:63328892-63328902 chr12:63328827-63328836 chr12:63328554-63328563
4	POLR2A	chr12:63327032-63327890	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:63327070-63328289	K562	blood:	n/a	n/a
6	TBP	chr12:63327408-63327638	K562	blood:	n/a	n/a
7	SIN3A	chr12:63326943-63329353	H1-hESC	embryonic stem cell:	n/a	chr12:63328666-63328677
8	POLR2A	chr12:63327043-63327571	MCF-7	breast:	n/a	n/a
9	BHLHE40	chr12:63326926-63329361	K562	blood:	n/a	chr12:63328948-63328964 chr12:63328794-63328810 chr12:63328667-63328683 chr12:63328526-63328542 chr12:63328523-63328539 chr12:63328885-63328901
10	E2F4	chr12:63327497-63327696	MCF10A-Er-Src	breast:	n/a	n/a
11	MAX	chr12:63326953-63329378	MCF-7	breast:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
12	POLR2A	chr12:63327131-63327894	HepG2	liver:	n/a	n/a
13	RCOR1	chr12:63326883-63329350	K562	blood:	n/a	n/a
14	KAP1	chr12:63326884-63328347	HEK293	kidney:	n/a	n/a
15	BACH1	chr12:63327254-63327630	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr12:63327428-63327612	H1-hESC	embryonic stem cell:	n/a	n/a
17	UBTF	chr12:63327533-63329210	K562	blood:	n/a	n/a
18	STAT3	chr12:63327491-63327710	MCF10A-Er-Src	breast:	n/a	n/a
19	HDAC2	chr12:63326945-63329435	MCF-7	breast:	n/a	chr12:63329372-63329386
20	CTBP2	chr12:63327020-63327863	H1-hESC	embryonic stem cell:	n/a	n/a
21	RCOR1	chr12:63327119-63328320	K562	blood:	n/a	n/a
22	HEY1	chr12:63326932-63327550	HepG2	liver:	n/a	n/a
23	SIN3AK20	chr12:63326856-63329407	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:62995343..62997102-chr12:63326865..63328948,2	K562	blood:
2	chr12:63325863..63329962-chr12:63356030..63360907,6	MCF-7	breast:
3	chr12:62996812..62998536-chr12:63327281..63329321,2	MCF-7	breast:
4	chr12:63244647..63247922-chr12:63326690..63328475,3	MCF-7	breast:
5	chr12:63326223..63329085-chr20:52208224..52210688,2	MCF-7	breast:
6	chr12:63278268..63280209-chr12:63326131..63327723,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252660	TF binding region
ENSG00000200296	Chromatin interaction
ENSG00000139239	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000199179	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000221949	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10506468	0.96[EUR][1000 genomes]
rs11174723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174731	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12301080	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12302398	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12302449	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12304611	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12311870	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12314057	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12315582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12316918	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1250152	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1666909	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1681992	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1681993	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1681994	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1695023	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17098649	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1731665	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2019497	0.83[EUR][1000 genomes]
rs2173441	0.95[ASN][1000 genomes]
rs2442110	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2628036	0.95[ASN][1000 genomes]
rs2628038	0.98[ASN][1000 genomes]
rs3858675	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58389317	0.96[EUR][1000 genomes]
rs58869921	0.96[EUR][1000 genomes]
rs699587	0.96[EUR][1000 genomes]
rs7314488	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314892	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7315141	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv899162	chr12:63279750-63334242	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	esv3355722	chr12:63327210-63330258	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	esv3378901	chr12:63327535-63330133	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63326400-63329200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:63326400-63329400	Active TSS	Brain Angular Gyrus	brain
3	chr12:63326600-63328200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:63326600-63329200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:63326600-63330000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr12:63326800-63327600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
7	chr12:63326800-63327600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
8	chr12:63326800-63327600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
9	chr12:63326800-63327800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
10	chr12:63326800-63327800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:63326800-63327800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr12:63326800-63327800	Bivalent/Poised TSS	Thymus	Thymus
13	chr12:63326800-63327800	Flanking Bivalent TSS/Enh	NH-A	brain
14	chr12:63326800-63328000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:63326800-63328200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:63326800-63328200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr12:63326800-63328200	Flanking Active TSS	Liver	Liver
18	chr12:63326800-63328200	Active TSS	Right Atrium	heart
19	chr12:63326800-63328400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr12:63326800-63328600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr12:63326800-63329000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:63326800-63329400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr12:63326800-63329400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr12:63326800-63329400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:63326800-63329400	Active TSS	Psoas Muscle	Psoas
26	chr12:63326800-63329400	Active TSS	Right Ventricle	heart
27	chr12:63326800-63329400	Active TSS	Stomach Mucosa	stomach
28	chr12:63326800-63329600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr12:63327000-63327600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
30	chr12:63327000-63327600	Active TSS	Colonic Mucosa	Colon
31	chr12:63327000-63327600	Enhancers	Spleen	Spleen
32	chr12:63327000-63327600	Flanking Bivalent TSS/Enh	NHLF	lung
33	chr12:63327000-63327800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:63327000-63327800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:63327000-63327800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr12:63327000-63327800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:63327000-63327800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
38	chr12:63327000-63327800	Flanking Active TSS	Hela-S3	cervix
39	chr12:63327000-63328000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:63327000-63328000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:63327000-63328000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr12:63327000-63328200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
43	chr12:63327000-63328200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
44	chr12:63327000-63328200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
45	chr12:63327000-63328200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr12:63327000-63328200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
47	chr12:63327000-63328200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
48	chr12:63327000-63328400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr12:63327000-63328400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
50	chr12:63327000-63328600	Flanking Active TSS	Primary hematopoietic stem cells	blood

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