Variant report

Variant	rs1165676
Chromosome Location	chr12:104322061-104322062
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	RUNX3	chr12:104321971-104325533	GM12878	blood:	n/a	n/a
2	NFIC	chr12:104322006-104324995	GM12878	blood:	n/a	n/a
3	FOXM1	chr12:104322048-104323502	GM12878	blood:	n/a	n/a
4	YY1	chr12:104321955-104322294	GM12892	blood:	n/a	chr12:104322088-104322098 chr12:104322088-104322110 chr12:104322089-104322097 chr12:104322087-104322099
5	RELA	chr12:104321990-104325291	GM19193	blood:	n/a	n/a
6	YY1	chr12:104321970-104322237	GM12891	blood:	n/a	chr12:104322088-104322098 chr12:104322088-104322110 chr12:104322089-104322097 chr12:104322087-104322099
7	MTA3	chr12:104321890-104325504	GM12878	blood:	n/a	n/a
8	RELA	chr12:104322051-104324458	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:104321945-104322327	GM12891	blood:	n/a	n/a
10	YY1	chr12:104321868-104322265	GM12892	blood:	n/a	chr12:104322088-104322098 chr12:104322088-104322110 chr12:104322089-104322097 chr12:104322087-104322099
11	BHLHE40	chr12:104322036-104324483	GM12878	blood:	n/a	n/a
12	ATF2	chr12:104321974-104325099	GM12878	blood:	n/a	n/a
13	SP1	chr12:104322007-104323607	GM12878	blood:	n/a	chr12:104323289-104323301
14	PML	chr12:104321903-104325251	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:104321755-104325879	GM12878	blood:	n/a	n/a
16	YY1	chr12:104321889-104322346	GM12878	blood:	n/a	chr12:104322088-104322098 chr12:104322088-104322110 chr12:104322089-104322097 chr12:104322087-104322099
17	RELA	chr12:104322015-104325092	GM18951	blood:	n/a	n/a
18	POLR2A	chr12:104321980-104325463	GM18526	blood:	n/a	n/a
19	RELA	chr12:104322058-104324482	GM18505	blood:	n/a	n/a
20	POLR2A	chr12:104320257-104326275	GM12878	blood:	n/a	n/a
21	STAT5A	chr12:104322043-104323967	GM12878	blood:	n/a	chr12:104323611-104323623 chr12:104323761-104323773 chr12:104322800-104322807
22	PAX5	chr12:104321924-104323423	GM12878	blood:	n/a	chr12:104323218-104323227
23	RELA	chr12:104322026-104324497	GM18526	blood:	n/a	n/a
24	YY1	chr12:104321828-104322299	GM12878	blood:	n/a	chr12:104322088-104322098 chr12:104322088-104322110 chr12:104322089-104322097 chr12:104322087-104322099
25	POLR2A	chr12:104321807-104325757	GM12892	blood:	n/a	n/a
26	POLR2A	chr12:104321980-104325932	GM19099	blood:	n/a	n/a
27	POLR2A	chr12:104322047-104327304	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:104321848-104325604	GM12892	blood:	n/a	n/a
29	YY1	chr12:104321962-104322602	GM12878	blood:	n/a	chr12:104322088-104322098 chr12:104322088-104322110 chr12:104322089-104322097 chr12:104322087-104322099
30	YY1	chr12:104322006-104322270	GM12891	blood:	n/a	chr12:104322088-104322098 chr12:104322088-104322110 chr12:104322089-104322097 chr12:104322087-104322099
31	EP300	chr12:104322030-104325136	GM12878	blood:	n/a	chr12:104324880-104324894 chr12:104323830-104323837
32	TBL1XR1	chr12:104322054-104325554	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:104321935-104326151	GM12891	blood:	n/a	n/a
34	POLR2A	chr12:104321941-104325434	GM15510	blood:	n/a	n/a
35	POLR2A	chr12:104321986-104322291	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:104322001-104325691	GM18505	blood:	n/a	n/a
37	RUNX3	chr12:104321988-104325055	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:104321998-104325551	GM18951	blood:	n/a	n/a
39	TCF12	chr12:104322016-104322323	GM12878	blood:	n/a	n/a
40	RELA	chr12:104322021-104325424	GM10847	blood:	n/a	n/a
41	POLR2A	chr12:104321952-104322251	GM12891	blood:	n/a	n/a
42	FOXM1	chr12:104321942-104325441	GM12878	blood:	n/a	n/a
43	IRF4	chr12:104321968-104322388	GM12878	blood:	n/a	n/a
44	SPI1	chr12:104322016-104322299	GM12891	blood:	n/a	n/a
45	POLR2A	chr12:104321950-104327416	GM12878	blood:	n/a	n/a
46	TCF3	chr12:104321983-104323440	GM12878	blood:	n/a	chr12:104322213-104322229 chr12:104322957-104322973
47	POLR2A	chr12:104321861-104325669	GM19193	blood:	n/a	n/a
48	POLR2A	chr12:104321944-104322290	GM12891	blood:	n/a	n/a
49	BATF	chr12:104322014-104323281	GM12878	blood:	n/a	n/a
50	NFATC1	chr12:104322030-104323531	GM12878	blood:	n/a	chr12:104323198-104323212

No.	Distal block	Cell Line	Cell type
1	chr12:104298858..104303101-chr12:104321689..104325332,4	K562	blood:
2	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:
3	chr12:104314809..104316668-chr12:104321304..104323532,2	MCF-7	breast:
4	chr12:104233715..104236918-chr12:104321893..104325386,6	K562	blood:
5	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
6	chr12:104309007..104311155-chr12:104321580..104324192,3	K562	blood:
7	chr12:104313655..104316610-chr12:104321073..104323844,5	MCF-7	breast:
8	chr12:104317968..104319875-chr12:104322035..104323737,2	MCF-7	breast:
9	chr12:104300678..104303599-chr12:104319392..104323559,4	K562	blood:
10	chr12:104294934..104297771-chr12:104321554..104323667,2	MCF-7	breast:

Variant related genes	Relation type
HSP90B1	TF binding region
MIR3652	TF binding region
ENSG00000204954	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000214198	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1165666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165673	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165682	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1165684	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1183212	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1866070	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866073	0.97[ASN][1000 genomes]
rs2722188	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104317200-104322600	Weak transcription	Aorta	Aorta
2	chr12:104317400-104322200	Weak transcription	Brain Anterior Caudate	brain
3	chr12:104318000-104322400	Weak transcription	Brain Substantia Nigra	brain
4	chr12:104318200-104322200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:104319200-104322200	Weak transcription	NHDF-Ad	bronchial
6	chr12:104319200-104322400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:104319400-104322200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:104319400-104322200	Weak transcription	A549	lung
9	chr12:104319400-104322400	Weak transcription	Osteobl	bone
10	chr12:104319400-104322600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:104319400-104323000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:104319600-104322200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:104319600-104322200	Weak transcription	HMEC	breast
14	chr12:104319600-104322400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:104319600-104322400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:104319600-104322400	Weak transcription	HSMM	muscle
17	chr12:104319600-104322400	Weak transcription	NHEK	skin
18	chr12:104319600-104322600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:104319600-104322600	Weak transcription	HSMMtube	muscle
20	chr12:104319800-104322600	Weak transcription	NH-A	brain
21	chr12:104320200-104322400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr12:104320800-104322600	Enhancers	Psoas Muscle	Psoas
23	chr12:104320800-104322800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr12:104321200-104322200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:104321200-104322200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:104321200-104322200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr12:104321200-104322200	Enhancers	Thymus	Thymus
28	chr12:104321200-104322200	Flanking Active TSS	GM12878-XiMat	blood
29	chr12:104321200-104322400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:104321200-104322400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:104321200-104322400	Enhancers	Adipose Nuclei	Adipose
32	chr12:104321200-104322400	Enhancers	Colonic Mucosa	Colon
33	chr12:104321200-104322400	Enhancers	Fetal Muscle Leg	muscle
34	chr12:104321200-104322600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr12:104321400-104322200	Enhancers	Primary B cells from peripheral blood	blood
36	chr12:104321400-104322200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:104321400-104322400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:104321400-104322400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr12:104321600-104322200	Enhancers	Primary T cells from cord blood	blood
40	chr12:104321600-104322200	Enhancers	Primary hematopoietic stem cells	blood
41	chr12:104321600-104322200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr12:104321600-104322800	Enhancers	Spleen	Spleen
43	chr12:104321800-104322200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr12:104322000-104322200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr12:104322000-104322200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr12:104322000-104322200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:104322000-104322200	Flanking Active TSS	Liver	Liver
48	chr12:104322000-104322200	Enhancers	Brain Hippocampus Middle	brain
49	chr12:104322000-104322200	Active TSS	Duodenum Mucosa	Duodenum
50	chr12:104322000-104322200	Enhancers	Fetal Intestine Large	intestine

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