Variant report

Variant	rs7975636
Chromosome Location	chr12:123943673-123943674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123942407-123943799	GM12892	blood:	n/a	n/a
2	EBF1	chr12:123943326-123943693	GM12878	blood:	n/a	chr12:123943502-123943513
3	JUN	chr12:123942323-123943713	K562	blood:	n/a	n/a
4	HEY1	chr12:123942533-123943695	K562	blood:	n/a	n/a
5	POLR2A	chr12:123942356-123943704	K562	blood:	n/a	n/a
6	POLR2A	chr12:123942385-123943678	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr12:123943263-123943796	HL-60	blood:	n/a	n/a
8	PML	chr12:123942305-123943765	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:123942547-123943813	K562	blood:	n/a	n/a
10	POLR2A	chr12:123942476-123943752	K562	blood:	n/a	n/a
11	SIN3AK20	chr12:123942366-123943713	MCF-7	breast:	n/a	n/a
12	EBF1	chr12:123943241-123943675	GM12878	blood:	n/a	chr12:123943502-123943513
13	POLR2A	chr12:123942334-123943711	H1-hESC	embryonic stem cell:	n/a	n/a
14	EBF1	chr12:123942893-123943684	GM12878	blood:	n/a	chr12:123943502-123943513
15	NR2F2	chr12:123943285-123943980	K562	blood:	n/a	n/a
16	ELF1	chr12:123942518-123943804	GM12878	blood:	n/a	chr12:123942683-123942695
17	ZNF263	chr12:123942589-123943718	HEK293-T-REx	kidney:	n/a	chr12:123942803-123942824
18	POLR2A	chr12:123942366-123943853	SK-N-MC	brain:	n/a	n/a
19	MAX	chr12:123942337-123943775	A549	lung:	n/a	chr12:123942792-123942801
20	MAX	chr12:123943217-123943741	K562	blood:	n/a	n/a
21	TAF1	chr12:123942408-123943708	H1-hESC	embryonic stem cell:	n/a	n/a
22	CUX1	chr12:123943436-123943838	K562	blood:	n/a	n/a
23	POLR2A	chr12:123942516-123943692	GM12892	blood:	n/a	n/a
24	POLR2A	chr12:123942553-123943811	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:123942528-123943689	GM18505	blood:	n/a	n/a
26	MTA3	chr12:123942350-123943749	GM12878	blood:	n/a	n/a
27	CUX1	chr12:123943463-123943815	GM12878	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123941578..123944282-chr12:124067320..124071098,9	MCF-7	breast:
2	chr12:123943032..123944561-chr12:124016969..124018583,2	MCF-7	breast:
3	chr12:123941486..123944276-chr12:124085171..124087519,2	K562	blood:
4	chr12:123873193..123874940-chr12:123942406..123944140,2	K562	blood:
5	chr12:123754868..123756621-chr12:123942711..123944463,2	MCF-7	breast:
6	chr12:123849365..123850946-chr12:123941525..123944430,2	K562	blood:
7	chr12:123866599..123869577-chr12:123942434..123944403,3	MCF-7	breast:
8	chr12:123756249..123757789-chr12:123941373..123944326,2	K562	blood:
9	chr12:123919998..123924322-chr12:123941781..123944675,4	K562	blood:
10	chr12:123942949..123945032-chr12:123947880..123951007,3	MCF-7	breast:
11	chr12:123873866..123876385-chr12:123942538..123944226,2	MCF-7	breast:
12	chr12:123868443..123871332-chr12:123941328..123944744,4	K562	blood:
13	chr12:123942564..123944577-chr12:124016063..124019666,4	MCF-7	breast:
14	chr12:123942486..123944135-chr12:124085124..124087552,2	MCF-7	breast:
15	chr12:123941098..123944051-chr12:124068238..124070527,2	K562	blood:
16	chr12:123941485..123944968-chr12:123948238..123952652,6	K562	blood:
17	chr12:123940979..123946241-chr12:123948686..123953480,7	MCF-7	breast:

No data

Variant related genes	Relation type
SNRNP35	TF binding region
ENSG00000183955	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000150977	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11497308	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11497312	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11497313	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11507739	1.00[ASN][1000 genomes]
rs11507744	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11516176	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11516178	1.00[ASN][1000 genomes]
rs11522340	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11534428	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11559494	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11560820	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13303266	1.00[ASN][1000 genomes]
rs13303358	1.00[ASN][1000 genomes]
rs28483351	1.00[ASN][1000 genomes]
rs28613273	1.00[ASN][1000 genomes]
rs28728075	1.00[ASN][1000 genomes]
rs28829651	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087496	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34031619	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35322317	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4047517	1.00[ASN][1000 genomes]
rs4078291	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4479070	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6606747	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300562	1.00[ASN][1000 genomes]
rs7315901	1.00[ASN][1000 genomes]
rs73412280	1.00[ASN][1000 genomes]
rs7978323	1.00[ASN][1000 genomes]
rs9330649	1.00[ASN][1000 genomes]
rs9330650	1.00[ASN][1000 genomes]
rs9697264	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9697459	1.00[ASN][1000 genomes]
rs9697616	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9697628	1.00[ASN][1000 genomes]
rs9697735	1.00[ASN][1000 genomes]
rs9723046	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9723192	1.00[ASN][1000 genomes]
rs9777813	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9778112	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[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	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	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers 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 miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers 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	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123942200-123943800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:123942200-123943800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:123942200-123943800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:123942200-123943800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:123942200-123943800	Active TSS	Fetal Stomach	stomach
6	chr12:123942200-123943800	Active TSS	Psoas Muscle	Psoas
7	chr12:123942200-123943800	Active TSS	Rectal Smooth Muscle	rectum
8	chr12:123942200-123943800	Active TSS	Right Ventricle	heart
9	chr12:123942200-123943800	Active TSS	Stomach Smooth Muscle	stomach
10	chr12:123942200-123943800	Active TSS	A549	lung
11	chr12:123942200-123944000	Active TSS	Duodenum Mucosa	Duodenum
12	chr12:123942200-123944000	Active TSS	Fetal Brain Female	brain
13	chr12:123942200-123944000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr12:123942200-123944200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:123942200-123944200	Active TSS	Hela-S3	cervix
16	chr12:123942200-123944600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:123942400-123943800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr12:123942400-123943800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr12:123942400-123943800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:123942400-123943800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:123942400-123943800	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr12:123942400-123943800	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr12:123942400-123943800	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr12:123942400-123943800	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr12:123942400-123943800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr12:123942400-123943800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:123942400-123943800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:123942400-123943800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:123942400-123943800	Active TSS	Aorta	Aorta
30	chr12:123942400-123943800	Active TSS	Brain Angular Gyrus	brain
31	chr12:123942400-123943800	Active TSS	Brain Anterior Caudate	brain
32	chr12:123942400-123943800	Active TSS	Brain Hippocampus Middle	brain
33	chr12:123942400-123943800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:123942400-123943800	Active TSS	Colon Smooth Muscle	Colon
35	chr12:123942400-123943800	Active TSS	Fetal Kidney	kidney
36	chr12:123942400-123943800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr12:123942400-123943800	Active TSS	Placenta Amnion	Placenta Amnion
38	chr12:123942400-123943800	Active TSS	HSMM	muscle
39	chr12:123942400-123943800	Active TSS	NH-A	brain
40	chr12:123942400-123943800	Active TSS	NHDF-Ad	bronchial
41	chr12:123942400-123943800	Active TSS	Osteobl	bone
42	chr12:123942400-123944000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:123942400-123944000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:123942400-123944000	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr12:123942400-123944000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:123942400-123944000	Active TSS	HMEC	breast
47	chr12:123942400-123944200	Active TSS	K562	blood
48	chr12:123942400-123944400	Active TSS	Primary T cells from cord blood	blood
49	chr12:123942400-123944400	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr12:123942400-123944400	Active TSS	GM12878-XiMat	blood

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