Variant report

Variant	rs10843839
Chromosome Location	chr12:30946119-30946120
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	MAX	chr12:30945474-30946250	A549	lung:	n/a	n/a
2	TCF12	chr12:30945437-30946233	A549	lung:	n/a	chr12:30945907-30945916
3	GATA1	chr12:30945205-30946586	PBDE	blood:	n/a	n/a
4	RCOR1	chr12:30945601-30946161	Hela-S3	cervix:	n/a	n/a
5	SP1	chr12:30945425-30946146	A549	lung:	n/a	n/a
6	TCF7L2	chr12:30945282-30946331	PANC-1	pancreas:	n/a	chr12:30945580-30945594 chr12:30945583-30945592 chr12:30945583-30945593 chr12:30945800-30945814 chr12:30945579-30945595 chr12:30945579-30945595
7	SMC3	chr12:30945155-30946215	Hela-S3	cervix:	n/a	n/a
8	SP1	chr12:30945485-30946264	A549	lung:	n/a	n/a
9	FOS	chr12:30945394-30946435	MCF10A-Er-Src	breast:	n/a	chr12:30946264-30946276 chr12:30946265-30946275
10	NFIC	chr12:30945347-30946485	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr12:30945363-30946253	ECC-1	luminal epithelium:	n/a	n/a
12	MAFK	chr12:30945564-30946304	Hela-S3	cervix:	n/a	chr12:30946267-30946276 chr12:30946263-30946277 chr12:30946262-30946278
13	GTF2F1	chr12:30945561-30946302	Hela-S3	cervix:	n/a	n/a
14	MAFK	chr12:30946077-30946469	IMR90	lung:	n/a	chr12:30946267-30946276 chr12:30946263-30946277 chr12:30946262-30946278
15	FOXA2	chr12:30945606-30946209	A549	lung:	n/a	n/a
16	TEAD4	chr12:30945618-30946188	A549	lung:	n/a	n/a
17	CEBPB	chr12:30945530-30946129	A549	lung:	n/a	n/a
18	TCF7L2	chr12:30945386-30946288	HCT-116	colon:	n/a	chr12:30945580-30945594 chr12:30945583-30945592 chr12:30945583-30945593 chr12:30945800-30945814 chr12:30945579-30945595 chr12:30945579-30945595
19	POLR2A	chr12:30945791-30946222	Hela-S3	cervix:	n/a	n/a
20	MYC	chr12:30946103-30946303	MCF10A-Er-Src	breast:	n/a	chr12:30946242-30946251
21	CHD2	chr12:30945561-30946127	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr12:30945530-30946304	Hela-S3	cervix:	n/a	n/a
23	STAT3	chr12:30945465-30946308	MCF10A-Er-Src	breast:	n/a	n/a
24	TCF12	chr12:30945398-30946513	ECC-1	luminal epithelium:	n/a	chr12:30945907-30945916 chr12:30946257-30946267
25	POLR2A	chr12:30945496-30946267	PANC-1	pancreas:	n/a	n/a
26	FOSL2	chr12:30945452-30946141	A549	lung:	n/a	n/a
27	SP1	chr12:30945336-30946416	HCT-116	colon:	n/a	n/a
28	GATA3	chr12:30945374-30946342	A549	lung:	n/a	n/a
29	TCF7L2	chr12:30945405-30946320	Hela-S3	cervix:	n/a	chr12:30945580-30945594 chr12:30945583-30945592 chr12:30945583-30945593 chr12:30945800-30945814 chr12:30945579-30945595 chr12:30945579-30945595
30	FOS	chr12:30945455-30946437	MCF10A-Er-Src	breast:	n/a	chr12:30946264-30946276 chr12:30946265-30946275
31	REST	chr12:30945434-30946152	A549	lung:	n/a	n/a
32	MAX	chr12:30945540-30946159	Hela-S3	cervix:	n/a	n/a
33	MAZ	chr12:30945978-30946191	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30940438..30941975-chr12:30944440..30946638,2	MCF-7	breast:

Variant related genes	Relation type
LINC00941	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10843840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843841	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11051078	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11051079	0.85[AMR][1000 genomes]
rs11051082	1.00[AMR][1000 genomes]
rs11051085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv34091	chr12:30927650-31061815	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30943800-30947600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:30943800-30947800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr12:30944000-30948200	Weak transcription	Left Ventricle	heart
4	chr12:30944400-30947600	Enhancers	HMEC	breast
5	chr12:30944400-30947600	Weak transcription	K562	blood
6	chr12:30944600-30947600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:30944800-30947000	Enhancers	Osteobl	bone
8	chr12:30945000-30946400	Enhancers	Fetal Muscle Leg	muscle
9	chr12:30945000-30947600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:30945000-30947600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:30945000-30947600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:30945000-30947600	Enhancers	HUVEC	blood vessel
13	chr12:30945000-30947800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:30945000-30948400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:30945200-30946200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr12:30945200-30946200	Flanking Active TSS	NHEK	skin
17	chr12:30945200-30946400	Enhancers	HSMMtube	muscle
18	chr12:30945200-30946600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr12:30945200-30946600	Flanking Active TSS	Hela-S3	cervix
20	chr12:30945200-30946600	Enhancers	HSMM	muscle
21	chr12:30945200-30947800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:30945200-30948000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:30945200-30948400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr12:30945200-30948400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:30945400-30946200	Enhancers	Stomach Mucosa	stomach
26	chr12:30945400-30946400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr12:30945400-30946600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr12:30945400-30946600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr12:30945400-30947600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:30945400-30947800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr12:30945400-30948200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr12:30945600-30946200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:30945600-30946400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:30945600-30946400	Flanking Active TSS	A549	lung
35	chr12:30945600-30946600	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr12:30945600-30946600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr12:30945600-30946600	Enhancers	NHDF-Ad	bronchial
38	chr12:30945600-30946600	Enhancers	NHLF	lung
39	chr12:30945600-30946800	Enhancers	HepG2	liver
40	chr12:30945600-30948200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:30945600-30948400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:30945800-30946200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr12:30945800-30946600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:30945800-30946600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr12:30945800-30946600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:30945800-30946600	Flanking Active TSS	NH-A	brain
47	chr12:30945800-30948400	Weak transcription	Esophagus	oesophagus
48	chr12:30945800-30948400	Weak transcription	Psoas Muscle	Psoas
49	chr12:30946000-30946200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:30946000-30946400	Enhancers	Fetal Muscle Trunk	muscle

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