Variant report

Variant	rs28492040
Chromosome Location	chr12:124017850-124017851
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:166)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:166 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:124017673-124018031	MCF-7	breast:	n/a	n/a
2	MAX	chr12:124017255-124019286	HepG2	liver:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
3	TCF12	chr12:124017638-124018148	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr12:124017557-124019155	K562	blood:	n/a	n/a
5	POLR2A	chr12:124017306-124019150	HepG2	liver:	n/a	n/a
6	TBL1XR1	chr12:124017265-124017940	K562	blood:	n/a	n/a
7	CBX3	chr12:124017259-124018108	K562	blood:	n/a	n/a
8	POLR2A	chr12:124017688-124019111	K562	blood:	n/a	n/a
9	MAX	chr12:124017326-124019119	K562	blood:	n/a	chr12:124017624-124017639
10	CEBPB	chr12:124017334-124018091	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:124017658-124018047	HepG2	liver:	n/a	n/a
12	MAZ	chr12:124017387-124018114	HepG2	liver:	n/a	chr12:124017624-124017639
13	ZNF143	chr12:124017375-124017974	Hela-S3	cervix:	n/a	n/a
14	MYC	chr12:124017825-124018090	K562	blood:	n/a	n/a
15	POLR2A	chr12:124017562-124019144	HUVEC	blood vessel:	n/a	n/a
16	RFX5	chr12:124017587-124018024	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr12:124017609-124018156	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:124017650-124018040	HepG2	liver:	n/a	n/a
19	HDAC2	chr12:124017608-124018022	HepG2	liver:	n/a	n/a
20	MAX	chr12:124017269-124019274	A549	lung:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
21	REST	chr12:124017537-124018039	A549	lung:	n/a	n/a
22	CREB1	chr12:124017473-124018163	A549	lung:	n/a	n/a
23	CHD2	chr12:124017413-124018001	K562	blood:	n/a	n/a
24	MYC	chr12:124017571-124018185	MCF-7	breast:	n/a	chr12:124017624-124017639
25	POLR2A	chr12:124017657-124018011	HCT-116	colon:	n/a	n/a
26	CHD2	chr12:124017754-124018058	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:124017727-124019089	K562	blood:	n/a	n/a
28	TAF1	chr12:124017566-124018105	HepG2	liver:	n/a	n/a
29	MYC	chr12:124017455-124018127	MCF10A-Er-Src	breast:	n/a	chr12:124017624-124017639
30	RCOR1	chr12:124016551-124018022	K562	blood:	n/a	n/a
31	ZMIZ1	chr12:124017276-124018020	K562	blood:	n/a	n/a
32	CCNT2	chr12:124017594-124018993	K562	blood:	n/a	chr12:124018745-124018754
33	MYC	chr12:124017675-124018126	HepG2	liver:	n/a	n/a
34	CTCF	chr12:124017834-124017873	MCF-7	breast:	n/a	n/a
35	POLR2A	chr12:124017631-124018155	Hela-S3	cervix:	n/a	n/a
36	GABPA	chr12:124017543-124017917	K562	blood:	n/a	chr12:124017630-124017639
37	BRCA1	chr12:124017418-124017970	Hela-S3	cervix:	n/a	n/a
38	MAX	chr12:124017459-124018605	Hela-S3	cervix:	n/a	chr12:124017624-124017639
39	POLR2A	chr12:124017559-124018108	H1-hESC	embryonic stem cell:	n/a	n/a
40	E2F6	chr12:124017363-124018308	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr12:124017667-124018046	Hela-S3	cervix:	n/a	n/a
42	MAZ	chr12:124016579-124019401	IMR90	lung:	n/a	chr12:124019137-124019147 chr12:124016824-124016835 chr12:124017249-124017259 chr12:124017624-124017639
43	NR2F2	chr12:124016531-124018094	K562	blood:	n/a	n/a
44	POLR2A	chr12:124017644-124019078	HepG2	liver:	n/a	n/a
45	MAX	chr12:124017303-124018190	H1-hESC	embryonic stem cell:	n/a	chr12:124017624-124017639
46	ELF1	chr12:124017362-124017936	K562	blood:	n/a	chr12:124017651-124017664
47	E2F6	chr12:124017502-124018246	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr12:124017651-124018533	Gliobla	brain:	n/a	n/a
49	YY1	chr12:124017655-124018125	K562	blood:	n/a	chr12:124017708-124017717
50	TBP	chr12:124017733-124018093	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123997284..124000079-chr12:124017073..124019484,2	MCF-7	breast:
2	chr12:124017823..124018449-chr6:26156256..26156790,2	HCT-116	colon:
3	chr12:124015709..124018064-chr12:124066858..124069100,3	MCF-7	breast:
4	chr12:123947470..123950375-chr12:124015636..124018854,3	K562	blood:
5	chr12:123872416..123876102-chr12:124017252..124019601,4	MCF-7	breast:
6	chr12:123871385..123875741-chr12:124017374..124019532,6	MCF-7	breast:
7	chr12:124017816..124019657-chr12:124117596..124119161,2	MCF-7	breast:
8	chr12:123753293..123757508-chr12:124015727..124020202,5	K562	blood:
9	chr12:124015786..124020200-chr12:124020787..124024805,6	K562	blood:
10	chr12:123942564..123944577-chr12:124016063..124019666,4	MCF-7	breast:
11	chr12:124016749..124018606-chr12:124069216..124071514,2	K562	blood:
12	chr12:123948940..123951509-chr12:124017235..124019368,2	MCF-7	breast:
13	chr12:123998884..124001416-chr12:124016546..124018370,2	K562	blood:
14	chr12:123943032..123944561-chr12:124016969..124018583,2	MCF-7	breast:
15	chr12:124017444..124019100-chr12:124084646..124086674,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3908	TF binding region
ENSG00000247373	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000266655	Chromatin interaction
ENSG00000086598	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13302918	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1533246	0.88[EUR][1000 genomes]
rs2333832	0.84[EUR][1000 genomes]
rs28604461	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647680	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28833471	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34734800	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016092	0.82[EUR][1000 genomes]
rs4930704	0.83[ASN][1000 genomes]
rs4930717	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953540	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953541	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488877	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6488878	0.84[EUR][1000 genomes]
rs7303956	0.86[EUR][1000 genomes]
rs7313751	0.83[ASN][1000 genomes]
rs7398935	0.83[ASN][1000 genomes]
rs7956299	0.83[ASN][1000 genomes]
rs7959714	0.83[EUR][1000 genomes]
rs7962151	0.83[ASN][1000 genomes]
rs7963804	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3357232	chr12:124017349-124019447	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124015400-124018000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr12:124016200-124018000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr12:124016400-124018000	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr12:124016400-124018000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr12:124016400-124018000	Flanking Active TSS	HMEC	breast
6	chr12:124016400-124019400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:124016600-124018000	Flanking Active TSS	Placenta	Placenta
8	chr12:124016800-124018000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
9	chr12:124016800-124018000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:124016800-124019000	Active TSS	Left Ventricle	heart
11	chr12:124016800-124019200	Active TSS	Aorta	Aorta
12	chr12:124016800-124019400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:124016800-124019400	Active TSS	Right Atrium	heart
14	chr12:124017000-124018000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr12:124017000-124018000	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr12:124017000-124018000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:124017000-124018000	Flanking Active TSS	Fetal Muscle Leg	muscle
18	chr12:124017000-124018200	Flanking Active TSS	Dnd41	blood
19	chr12:124017000-124019000	Active TSS	NHDF-Ad	bronchial
20	chr12:124017000-124019200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:124017000-124019200	Active TSS	Ovary	ovary
22	chr12:124017000-124019200	Active TSS	Psoas Muscle	Psoas
23	chr12:124017000-124019200	Active TSS	Right Ventricle	heart
24	chr12:124017000-124019200	Active TSS	NHLF	lung
25	chr12:124017000-124019400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:124017000-124019400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:124017000-124019600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:124017200-124018000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:124017200-124018000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:124017200-124019000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:124017200-124019000	Active TSS	Brain Cingulate Gyrus	brain
32	chr12:124017200-124019000	Active TSS	A549	lung
33	chr12:124017200-124019400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr12:124017200-124019400	Active TSS	Colon Smooth Muscle	Colon
35	chr12:124017200-124019400	Active TSS	HSMM	muscle
36	chr12:124017400-124018000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:124017400-124018000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:124017400-124018000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:124017400-124018000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
40	chr12:124017400-124018000	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr12:124017400-124018000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr12:124017400-124018000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:124017400-124018000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr12:124017400-124018000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr12:124017400-124018000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr12:124017400-124018000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:124017400-124018000	Flanking Active TSS	Colonic Mucosa	Colon
48	chr12:124017400-124018000	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr12:124017400-124018000	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr12:124017400-124018000	Flanking Active TSS	Fetal Intestine Small	intestine

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