Variant report

Variant	rs35009941
Chromosome Location	chr12:104682528-104682529
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:516)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:516 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:104682421-104682774	K562	blood:	n/a	n/a
2	BRCA1	chr12:104682117-104683361	Hela-S3	cervix:	n/a	n/a
3	RUNX3	chr12:104682396-104683047	GM12878	blood:	n/a	n/a
4	GATA3	chr12:104681970-104683989	A549	lung:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683191-104683199 chr12:104683216-104683229 chr12:104683841-104683851 chr12:104683193-104683210
5	POLR2A	chr12:104679566-104684466	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr12:104682363-104683011	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr12:104682395-104683011	A549	lung:	n/a	n/a
8	PML	chr12:104682117-104682969	K562	blood:	n/a	n/a
9	MAFF	chr12:104682249-104682677	HepG2	liver:	n/a	n/a
10	CREB1	chr12:104682307-104683211	GM12878	blood:	n/a	n/a
11	MXI1	chr12:104682382-104682855	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOXA1	chr12:104682371-104682799	T-47D	breast:	n/a	n/a
13	WRNIP1	chr12:104682017-104683835	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:104680676-104684470	A549	lung:	n/a	n/a
15	POLR2A	chr12:104682049-104683470	K562	blood:	n/a	n/a
16	SMC3	chr12:104682500-104682829	GM12878	blood:	n/a	n/a
17	EBF1	chr12:104682426-104682856	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:104682473-104682947	Gliobla	brain:	n/a	n/a
19	POLR2A	chr12:104679817-104683502	Hela-S3	cervix:	n/a	n/a
20	SIN3AK20	chr12:104682385-104682937	K562	blood:	n/a	n/a
21	MYC	chr12:104682374-104683014	K562	blood:	n/a	n/a
22	YY1	chr12:104682483-104682714	HCT-116	colon:	n/a	n/a
23	POLR2A	chr12:104679670-104683975	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr12:104682387-104683013	GM19099	blood:	n/a	n/a
25	RCOR1	chr12:104682193-104682885	K562	blood:	n/a	n/a
26	GATA3	chr12:104682287-104683460	SK-N-SH	brain:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683191-104683199 chr12:104683216-104683229 chr12:104683193-104683210
27	POLR2A	chr12:104682338-104682966	NB4	blood:	n/a	n/a
28	POLR2A	chr12:104682066-104683608	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr12:104682386-104682983	GM15510	blood:	n/a	n/a
30	SIN3AK20	chr12:104682395-104682908	PFSK-1	brain:	n/a	n/a
31	SIN3AK20	chr12:104682350-104682781	H1-hESC	embryonic stem cell:	n/a	n/a
32	IRF1	chr12:104682155-104682890	K562	blood:	n/a	n/a
33	POLR2A	chr12:104682326-104682929	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr12:104682324-104683039	HL-60	blood:	n/a	n/a
35	POLR2A	chr12:104682402-104682981	GM12878	blood:	n/a	n/a
36	CTCF	chr12:104682460-104682610	HepG2	liver:	n/a	n/a
37	SP1	chr12:104679158-104684055	A549	lung:	n/a	chr12:104682628-104682639 chr12:104683086-104683100
38	CTCF	chr12:104682500-104682650	AG09319	gingival:	n/a	n/a
39	SIN3AK20	chr12:104682283-104683003	PANC-1	pancreas:	n/a	n/a
40	BCL3	chr12:104681838-104683936	A549	lung:	n/a	n/a
41	NR3C1	chr12:104682334-104682919	A549	lung:	n/a	n/a
42	POLR2A	chr12:104679672-104683881	HepG2	liver:	n/a	n/a
43	MYC	chr12:104682273-104683291	NB4	blood:	n/a	n/a
44	STAT3	chr12:104682357-104682990	MCF10A-Er-Src	breast:	n/a	n/a
45	MAX	chr12:104682079-104683156	ECC-1	luminal epithelium:	n/a	n/a
46	FOXA1	chr12:104682343-104682821	HepG2	liver:	n/a	n/a
47	POLR2A	chr12:104682141-104682954	K562	blood:	n/a	n/a
48	YY1	chr12:104682371-104682994	K562	blood:	n/a	chr12:104682480-104682489
49	POU2F2	chr12:104682320-104683006	GM12878	blood:	n/a	n/a
50	HDAC2	chr12:104682360-104682971	HepG2	liver:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104359459..104362433-chr12:104679529..104682592,4	K562	blood:
2	chr12:104680883..104682793-chr4:2937932..2939461,2	MCF-7	breast:
3	chr12:104348328..104351209-chr12:104680724..104683661,2	K562	blood:
4	chr12:104680142..104683904-chr12:104694272..104698636,5	MCF-7	breast:
5	chr12:104678772..104682731-chr12:105498551..105503490,6	K562	blood:
6	chr12:104608375..104610840-chr12:104681920..104683609,3	MCF-7	breast:
7	chr12:104441752..104444274-chr12:104682358..104684016,2	K562	blood:
8	chr12:104681104..104682731-chr12:105500276..105502937,2	K562	blood:
9	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:
10	chr12:104606650..104611349-chr12:104679680..104683932,8	K562	blood:
11	chr12:104643850..104647465-chr12:104679926..104684172,5	K562	blood:
12	chr12:104530429..104534144-chr12:104679811..104684673,6	MCF-7	breast:
13	chr12:104681941..104682582-chrX:153284861..153285557,2	Hela-S3	cervix:
14	chr12:104643349..104645898-chr12:104680595..104683102,2	K562	blood:
15	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:
16	chr12:104681662..104683943-chr12:104703194..104704714,2	MCF-7	breast:

No data

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000198431	Chromatin interaction
ENSG00000184216	Chromatin interaction
ENSG00000120820	Chromatin interaction
ENSG00000255150	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000211524	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11111949	1.00[EUR][1000 genomes]
rs11111970	0.94[ASN][1000 genomes]
rs11111973	0.94[ASN][1000 genomes]
rs11832165	1.00[EUR][1000 genomes]
rs11832923	1.00[EUR][1000 genomes]
rs11833441	1.00[EUR][1000 genomes]
rs12299988	1.00[EUR][1000 genomes]
rs12312443	1.00[EUR][1000 genomes]
rs12318033	0.94[ASN][1000 genomes]
rs12368657	0.94[ASN][1000 genomes]
rs34407590	0.94[ASN][1000 genomes]
rs34518697	1.00[ASN][1000 genomes]
rs34612644	1.00[ASN][1000 genomes]
rs35456434	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35472124	1.00[ASN][1000 genomes]
rs35531900	1.00[EUR][1000 genomes]
rs35764486	1.00[ASN][1000 genomes]
rs41453549	1.00[EUR][1000 genomes]
rs4576900	1.00[ASN][1000 genomes]
rs4964753	0.94[ASN][1000 genomes]
rs58078551	1.00[ASN][1000 genomes]
rs58716236	1.00[ASN][1000 genomes]
rs60333117	1.00[EUR][1000 genomes]
rs61109788	1.00[EUR][1000 genomes]
rs7303284	1.00[ASN][1000 genomes]
rs7309973	1.00[ASN][1000 genomes]
rs7958103	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 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	chr12:104680000-104683200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:104680000-104683400	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr12:104680000-104683600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:104680000-104683800	Active TSS	Aorta	Aorta
5	chr12:104680200-104682600	Active TSS	Brain Germinal Matrix	brain
6	chr12:104680200-104683200	Active TSS	Brain Substantia Nigra	brain
7	chr12:104680400-104683000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:104680400-104683000	Active TSS	Brain Angular Gyrus	brain
9	chr12:104680400-104683000	Active TSS	Fetal Brain Male	brain
10	chr12:104680400-104683200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:104680400-104683200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:104680400-104683200	Active TSS	Colon Smooth Muscle	Colon
13	chr12:104680400-104683200	Active TSS	Fetal Brain Female	brain
14	chr12:104680400-104683400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:104680400-104683400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:104680400-104683600	Active TSS	Brain Anterior Caudate	brain
17	chr12:104680400-104683600	Active TSS	Brain Cingulate Gyrus	brain
18	chr12:104680400-104683600	Active TSS	Brain Hippocampus Middle	brain
19	chr12:104680400-104683600	Active TSS	Fetal Kidney	kidney
20	chr12:104680400-104683600	Active TSS	Left Ventricle	heart
21	chr12:104680400-104683600	Active TSS	Ovary	ovary
22	chr12:104680400-104683600	Active TSS	Psoas Muscle	Psoas
23	chr12:104680400-104683600	Active TSS	Right Ventricle	heart
24	chr12:104680400-104683800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr12:104680400-104684000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr12:104680400-104684000	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr12:104680400-104684000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr12:104680400-104684200	Active TSS	Right Atrium	heart
29	chr12:104680600-104682600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:104680600-104682600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:104680600-104682600	Active TSS	NHLF	lung
32	chr12:104680600-104682800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:104680600-104682800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr12:104680600-104682800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:104680600-104682800	Active TSS	Fetal Thymus	thymus
36	chr12:104680600-104682800	Active TSS	K562	blood
37	chr12:104680600-104682800	Active TSS	Osteobl	bone
38	chr12:104680600-104683000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:104680600-104683000	Active TSS	Small Intestine	intestine
40	chr12:104680600-104683000	Active TSS	HSMMtube	muscle
41	chr12:104680600-104683000	Active TSS	HUVEC	blood vessel
42	chr12:104680600-104683200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:104680600-104683200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:104680600-104683200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:104680600-104683200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:104680600-104683200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:104680600-104683200	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr12:104680600-104683200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:104680600-104683200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr12:104680600-104683200	Active TSS	Fetal Intestine Large	intestine

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