Variant report

Variant	rs10467099
Chromosome Location	chr12:48228364-48228365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
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	ATF1	chr12:48228092-48228806	K562	blood:	n/a	n/a
2	RCOR1	chr12:48228137-48228683	K562	blood:	n/a	n/a
3	ZNF143	chr12:48228080-48228674	K562	blood:	n/a	n/a
4	POLR2A	chr12:48228309-48228921	K562	blood:	n/a	n/a
5	GATA1	chr12:48227197-48228933	PBDE	blood:	n/a	chr12:48228611-48228620
6	IRF1	chr12:48227440-48228858	K562	blood:	n/a	chr12:48228785-48228798 chr12:48228770-48228779
7	EP300	chr12:48226878-48228863	K562	blood:	n/a	n/a
8	TBL1XR1	chr12:48227369-48228859	K562	blood:	n/a	n/a
9	BHLHE40	chr12:48227514-48228389	K562	blood:	n/a	n/a
10	MAZ	chr12:48227971-48228878	K562	blood:	n/a	n/a
11	POLR2A	chr12:48225808-48231662	Raji	blood:	n/a	n/a
12	CEBPB	chr12:48228165-48228570	K562	blood:	n/a	n/a
13	MAFF	chr12:48228293-48228593	K562	blood:	n/a	n/a
14	TEAD4	chr12:48226963-48228799	K562	blood:	n/a	chr12:48227797-48227806
15	POLR2A	chr12:48228003-48228917	K562	blood:	n/a	n/a
16	NR2F2	chr12:48227984-48228461	K562	blood:	n/a	n/a
17	POLR2A	chr12:48228013-48229849	K562	blood:	n/a	n/a
18	MAFK	chr12:48228314-48228634	K562	blood:	n/a	n/a
19	ARID3A	chr12:48228091-48228742	K562	blood:	n/a	n/a
20	JUND	chr12:48226815-48228864	K562	blood:	n/a	n/a
21	MAX	chr12:48227424-48228578	K562	blood:	n/a	chr12:48227879-48227888
22	MYC	chr12:48226785-48228939	K562	blood:	n/a	chr12:48227879-48227888
23	CBX3	chr12:48227892-48228483	K562	blood:	n/a	n/a
24	IRF1	chr12:48228180-48228892	K562	blood:	n/a	chr12:48228785-48228798 chr12:48228770-48228779
25	ZC3H11A	chr12:48227870-48228464	K562	blood:	n/a	n/a
26	MYC	chr12:48227382-48228714	K562	blood:	n/a	chr12:48227879-48227888
27	CCNT2	chr12:48228168-48228866	K562	blood:	n/a	chr12:48228600-48228609
28	MAX	chr12:48227902-48228567	K562	blood:	n/a	n/a
29	TAL1	chr12:48227428-48228780	K562	blood:	n/a	n/a
30	BACH1	chr12:48228199-48228514	K562	blood:	n/a	n/a
31	CHD2	chr12:48228057-48228564	K562	blood:	n/a	n/a
32	POLR2A	chr12:48228242-48228751	K562	blood:	n/a	n/a
33	RCOR1	chr12:48226786-48228887	K562	blood:	n/a	n/a
34	UBTF	chr12:48228005-48228691	K562	blood:	n/a	n/a
35	UBTF	chr12:48228015-48228790	K562	blood:	n/a	n/a
36	CUX1	chr12:48228311-48228615	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48221708..48225796-chr12:48227739..48231535,5	MCF-7	breast:
2	chr12:48167054..48169032-chr12:48227941..48229658,2	MCF-7	breast:
3	chr12:48227911..48229940-chr12:48244103..48245883,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC48A1-2	chr12:48228022-48228434	ENSG00000257488
2	lnc-SLC48A1-2	chr12:48228022-48228498	ENSG00000257488

No data

Variant related genes	Relation type
HDAC7	TF binding region
ENSG00000257488	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11168263	0.83[AMR][1000 genomes]
rs11574097	0.83[AMR][1000 genomes]
rs11574100	0.83[AMR][1000 genomes]
rs11574118	0.83[AMR][1000 genomes]
rs11574141	0.83[AMR][1000 genomes]
rs12299534	0.83[AMR][1000 genomes]
rs12308082	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48218800-48229000	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr12:48219000-48228800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:48222200-48229800	Enhancers	Primary B cells from cord blood	blood
4	chr12:48223200-48228600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:48223200-48229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:48223400-48229800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:48223400-48232200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:48223400-48236800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:48223400-48237000	Weak transcription	Colonic Mucosa	Colon
10	chr12:48223600-48228800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:48223600-48228800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:48223600-48228800	Weak transcription	Fetal Heart	heart
13	chr12:48223600-48229400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:48223600-48229400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:48223600-48231200	Weak transcription	A549	lung
16	chr12:48223600-48231800	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:48223600-48237000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:48223600-48238600	Weak transcription	Right Atrium	heart
19	chr12:48223600-48239800	Weak transcription	Gastric	stomach
20	chr12:48223800-48228800	Weak transcription	NHEK	skin
21	chr12:48224200-48228800	Weak transcription	HMEC	breast
22	chr12:48224200-48229400	Flanking Active TSS	Fetal Thymus	thymus
23	chr12:48224200-48232200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:48224200-48232600	Weak transcription	Psoas Muscle	Psoas
25	chr12:48224200-48238400	Weak transcription	NHDF-Ad	bronchial
26	chr12:48224400-48228400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:48224400-48229400	Weak transcription	Adipose Nuclei	Adipose
28	chr12:48224600-48229200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:48224600-48229800	Weak transcription	Right Ventricle	heart
30	chr12:48224600-48238000	Weak transcription	Esophagus	oesophagus
31	chr12:48224800-48229000	Flanking Active TSS	Thymus	Thymus
32	chr12:48225400-48231800	Enhancers	Primary hematopoietic stem cells	blood
33	chr12:48225600-48228600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:48225600-48231800	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:48225800-48228800	Enhancers	Dnd41	blood
36	chr12:48225800-48230400	Enhancers	Fetal Muscle Leg	muscle
37	chr12:48225800-48231800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:48226000-48228800	Enhancers	Fetal Muscle Trunk	muscle
39	chr12:48226000-48230000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:48226000-48230000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:48226000-48231400	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr12:48226600-48228800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:48226800-48228800	Flanking Active TSS	K562	blood
44	chr12:48226800-48231000	Enhancers	GM12878-XiMat	blood
45	chr12:48227000-48229000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:48227000-48229000	Enhancers	Spleen	Spleen
47	chr12:48227000-48230400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr12:48227000-48233800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr12:48227200-48228800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:48227200-48232400	Enhancers	Primary T helper cells PMA-I stimulated	--

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