Variant report

Variant	rs73417343
Chromosome Location	chr12:123722568-123722569
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	RCOR1	chr12:123722295-123722729	GM12878	blood:	n/a	n/a
2	RAD21	chr12:123722447-123723250	SK-N-SH	brain:	n/a	chr12:123722818-123722832 chr12:123722814-123722833 chr12:123722823-123722832
3	PAX5	chr12:123722118-123722652	GM12891	blood:	n/a	n/a
4	CTCF	chr12:123722471-123723174	SK-N-SH	brain:	n/a	chr12:123722817-123722833 chr12:123722811-123722832 chr12:123722816-123722834 chr12:123722818-123722831 chr12:123722823-123722831
5	STAT5A	chr12:123721930-123722973	GM12878	blood:	n/a	n/a
6	RAD21	chr12:123722430-123723235	HCT-116	colon:	n/a	chr12:123722818-123722832 chr12:123722814-123722833 chr12:123722823-123722832
7	RUNX3	chr12:123721926-123723025	GM12878	blood:	n/a	n/a
8	RAD21	chr12:123722546-123723000	SK-N-SH_RA	brain:	n/a	chr12:123722818-123722832 chr12:123722814-123722833 chr12:123722823-123722832
9	BCLAF1	chr12:123721858-123723038	GM12878	blood:	n/a	n/a
10	MEF2A	chr12:123721836-123722616	GM12878	blood:	n/a	n/a
11	RAD21	chr12:123722549-123722934	H1-hESC	embryonic stem cell:	n/a	chr12:123722818-123722832 chr12:123722814-123722833 chr12:123722823-123722832
12	RUNX3	chr12:123721973-123722858	GM12878	blood:	n/a	n/a
13	PAX5	chr12:123722095-123722592	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:123722445-123722641	K562	blood:	n/a	n/a
15	CTCF	chr12:123722480-123722630	GM06990	blood:	n/a	n/a
16	ZNF384	chr12:123722204-123722869	GM12878	blood:	n/a	n/a
17	CTCF	chr12:123722183-123723420	A549	lung:	n/a	chr12:123722817-123722833 chr12:123722811-123722832 chr12:123722816-123722834 chr12:123722818-123722831 chr12:123722823-123722831
18	CTCF	chr12:123722527-123723019	MCF-7	breast:	n/a	chr12:123722817-123722833 chr12:123722811-123722832 chr12:123722816-123722834 chr12:123722818-123722831 chr12:123722823-123722831
19	CTCF	chr12:123722497-123723175	HCT-116	colon:	n/a	chr12:123722817-123722833 chr12:123722811-123722832 chr12:123722816-123722834 chr12:123722818-123722831 chr12:123722823-123722831
20	MTA3	chr12:123721211-123723033	GM12878	blood:	n/a	n/a
21	RAD21	chr12:123722536-123723058	HepG2	liver:	n/a	chr12:123722818-123722832 chr12:123722814-123722833 chr12:123722823-123722832
22	MTA3	chr12:123721837-123722604	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:123721337-123722769	HepG2	liver:	n/a	n/a
24	CEBPB	chr12:123721535-123723150	GM12878	blood:	n/a	n/a
25	CTCF	chr12:123722480-123722630	HAc	cerebellar:	n/a	n/a
26	NFATC1	chr12:123721928-123723023	GM12878	blood:	n/a	n/a
27	RAD21	chr12:123722446-123723072	HCT-116	colon:	n/a	chr12:123722818-123722832 chr12:123722814-123722833 chr12:123722823-123722832
28	RAD21	chr12:123722553-123723056	H1-hESC	embryonic stem cell:	n/a	chr12:123722818-123722832 chr12:123722814-123722833 chr12:123722823-123722832
29	RAD21	chr12:123722505-123723127	MCF-7	breast:	n/a	chr12:123722818-123722832 chr12:123722814-123722833 chr12:123722823-123722832
30	ATF2	chr12:123721847-123723074	GM12878	blood:	n/a	n/a
31	NFIC	chr12:123721951-123723010	GM12878	blood:	n/a	n/a
32	PML	chr12:123721863-123722830	GM12878	blood:	n/a	n/a
33	RAD21	chr12:123722497-123723160	A549	lung:	n/a	chr12:123722818-123722832 chr12:123722814-123722833 chr12:123722823-123722832
34	CTCF	chr12:123722536-123722928	K562	blood:	n/a	chr12:123722817-123722833 chr12:123722811-123722832 chr12:123722816-123722834 chr12:123722818-123722831 chr12:123722823-123722831
35	SMC3	chr12:123722415-123723652	SK-N-SH	brain:	n/a	chr12:123722818-123722832
36	YY1	chr12:123722321-123722614	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123717076..123718967-chr12:123720807..123722850,2	MCF-7	breast:
2	chr12:123527755..123528597-chr12:123722388..123723377,4	MCF-7	breast:
3	chr12:123527734..123528656-chr12:123722305..123723382,7	MCF-7	breast:
4	chr12:123350122..123350678-chr12:123722363..123722904,2	MCF-7	breast:
5	chr12:123449911..123452361-chr12:123721707..123723952,2	MCF-7	breast:
6	chr12:123436582..123437364-chr12:123722407..123722993,2	MCF-7	breast:
7	chr12:123715385..123717743-chr12:123720225..123722840,2	MCF-7	breast:
8	chr12:123525430..123528340-chr12:123721388..123723225,2	MCF-7	breast:
9	chr12:123715079..123721002-chr12:123721919..123730378,16	K562	blood:
10	chr12:123459434..123462270-chr12:123721239..123724536,4	MCF-7	breast:
11	chr12:123721738..123724481-chr12:123725404..123728310,3	K562	blood:
12	chr12:123722318..123723838-chr12:123725541..123727819,2	MCF-7	breast:
13	chr12:123462884..123465858-chr12:123721353..123723553,2	MCF-7	breast:

Variant related genes	Relation type
MPHOSPH9	TF binding region
ENSG00000182196	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000256028	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000111325	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56910713	0.85[AMR][1000 genomes]
rs58339539	0.86[AFR][1000 genomes]
rs59708426	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7299155	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73417342	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73417346	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73417348	0.86[AFR][1000 genomes];1.00[AMR][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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS 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 target site	53 gene(s)	inside rSNPs	diseases
3	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123718800-123728400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:123718800-123733000	Weak transcription	Esophagus	oesophagus
4	chr12:123718800-123733800	Weak transcription	Aorta	Aorta
5	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
6	chr12:123719000-123722600	Weak transcription	Placenta	Placenta
7	chr12:123719000-123724400	Weak transcription	HSMM	muscle
8	chr12:123719000-123725000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:123719000-123725400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:123719000-123725400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:123719000-123726200	Weak transcription	Right Ventricle	heart
12	chr12:123719000-123726200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:123719000-123726800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:123719000-123728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:123719000-123731600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:123719000-123732600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:123719200-123723200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:123719200-123725800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:123719200-123726600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:123719200-123733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:123719200-123735200	Weak transcription	Ovary	ovary
23	chr12:123719400-123723400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
24	chr12:123719400-123726600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:123719600-123723200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:123719600-123726400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:123719600-123734200	Weak transcription	Colonic Mucosa	Colon
28	chr12:123719600-123738400	Weak transcription	NH-A	brain
29	chr12:123719800-123723200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr12:123719800-123723400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:123719800-123726200	Weak transcription	Fetal Lung	lung
32	chr12:123719800-123726400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:123719800-123726600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:123719800-123726800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:123719800-123726800	Weak transcription	NHDF-Ad	bronchial
36	chr12:123719800-123728800	Strong transcription	Fetal Stomach	stomach
37	chr12:123719800-123733600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:123719800-123733600	Weak transcription	Spleen	Spleen
39	chr12:123719800-123733800	Weak transcription	Fetal Intestine Large	intestine
40	chr12:123720000-123722800	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:123720000-123723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:123720000-123723200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr12:123720000-123723200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:123720000-123723600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr12:123720000-123726200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:123720000-123726200	Weak transcription	Psoas Muscle	Psoas
47	chr12:123720000-123726400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr12:123720000-123726400	Weak transcription	Adipose Nuclei	Adipose
49	chr12:123720000-123726400	Weak transcription	Brain Angular Gyrus	brain
50	chr12:123720000-123726400	Weak transcription	Brain Anterior Caudate	brain

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