Variant report

Variant	rs73071293
Chromosome Location	chr12:25347780-25347781
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	MXI1	chr12:25347216-25349605	SK-N-SH	brain:	n/a	chr12:25348081-25348096
2	POLR2A	chr12:25347504-25348981	HepG2	liver:	n/a	n/a
3	FOXM1	chr12:25347744-25348767	GM12878	blood:	n/a	n/a
4	BCL3	chr12:25347759-25348635	A549	lung:	n/a	chr12:25348126-25348139
5	HCFC1	chr12:25347139-25349028	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:25347727-25349494	PBDE	blood:	n/a	n/a
7	SIN3AK20	chr12:25347638-25348659	MCF-7	breast:	n/a	n/a
8	REST	chr12:25347724-25349021	H1-neurons	neurons:	n/a	chr12:25348109-25348127
9	SP1	chr12:25347774-25348520	A549	lung:	n/a	chr12:25348097-25348107 chr12:25348157-25348171 chr12:25348096-25348108 chr12:25348157-25348166 chr12:25348156-25348168 chr12:25348097-25348106 chr12:25348157-25348167 chr12:25348157-25348166 chr12:25348158-25348167 chr12:25348096-25348108 chr12:25348157-25348167 chr12:25348098-25348107 chr12:25348097-25348107 chr12:25348156-25348168
10	SIN3A	chr12:25347727-25348885	H1-hESC	embryonic stem cell:	n/a	n/a
11	MYC	chr12:25347712-25349022	NB4	blood:	n/a	chr12:25348097-25348107
12	MAZ	chr12:25347583-25348872	IMR90	lung:	n/a	chr12:25348097-25348107
13	TAF1	chr12:25347757-25348607	H1-hESC	embryonic stem cell:	n/a	n/a
14	NRF1	chr12:25347594-25348952	SK-N-SH	brain:	n/a	chr12:25348098-25348107 chr12:25348158-25348167
15	WRNIP1	chr12:25347748-25348495	GM12878	blood:	n/a	n/a
16	ELK4	chr12:25347683-25348279	Hela-S3	cervix:	n/a	chr12:25348141-25348152
17	MAZ	chr12:25347524-25348803	HepG2	liver:	n/a	chr12:25348097-25348107
18	SIN3AK20	chr12:25347760-25348427	H1-hESC	embryonic stem cell:	n/a	n/a
19	YY1	chr12:25347619-25348061	H1-hESC	embryonic stem cell:	n/a	n/a
20	SIN3AK20	chr12:25347656-25348624	PANC-1	pancreas:	n/a	n/a
21	SIN3AK20	chr12:25347637-25348518	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr12:25347604-25351824	MCF10A-Er-Src	breast:	n/a	n/a
23	GABPA	chr12:25347775-25348577	MCF-7	breast:	n/a	chr12:25348098-25348107 chr12:25348158-25348167
24	FOXA2	chr12:25347740-25348521	A549	lung:	n/a	n/a
25	POLR2A	chr12:25347050-25349790	MCF10A-Er-Src	breast:	n/a	n/a
26	MXI1	chr12:25347747-25348605	HepG2	liver:	n/a	chr12:25348081-25348096
27	POLR2A	chr12:25347626-25349096	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3AK20	chr12:25347708-25348131	K562	blood:	n/a	n/a
29	POLR2A	chr12:25347773-25348714	Hela-S3	cervix:	n/a	n/a
30	BHLHE40	chr12:25347720-25349016	K562	blood:	n/a	n/a
31	POLR2A	chr12:25347634-25349053	IMR90	lung:	n/a	n/a
32	POLR2A	chr12:25347748-25347817	Gliobla	brain:	n/a	n/a
33	PML	chr12:25347737-25348708	GM12878	blood:	n/a	n/a
34	GTF2F1	chr12:25347729-25348402	K562	blood:	n/a	n/a
35	RCOR1	chr12:25347673-25348559	K562	blood:	n/a	n/a
36	NRF1	chr12:25347398-25348714	GM12878	blood:	n/a	chr12:25348098-25348107 chr12:25348158-25348167
37	YY1	chr12:25347707-25347971	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr12:25347757-25348887	K562	blood:	n/a	n/a
39	POLR2A	chr12:25347716-25348626	SK-N-MC	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:25347752-25347802	BE2_C	brain:	n/a
2	chr12:25347752-25347802	H1-hESC	embryonic stem cell:	embryo
3	chr12:25347752-25347802	HMEC	breast:	n/a
4	chr12:25347752-25347802	LNCaP	prostate:	n/a
5	chr12:25347752-25347802	RPTEC	kidney:	n/a
6	chr12:25347752-25347802	AG04449	skin:	fetal
7	chr12:25347752-25347802	PANC-1	pancreas:	n/a
8	chr12:25347752-25347802	AG09319	gingival:	n/a
9	chr12:25347752-25347802	HAEpiC	amniotic membrane:	n/a
10	chr12:25347752-25347802	HRE	kidney:	n/a
11	chr12:25347752-25347802	GM12892	blood:	n/a
12	chr12:25347752-25347802	HRCEpiC	kidney:	n/a
13	chr12:25347752-25347802	HPAEpiC	pulmonary alveolar:	n/a
14	chr12:25347752-25347802	GM06990	blood:	n/a
15	chr12:25347752-25347802	NH-A	brain:	n/a
16	chr12:25347752-25347802	SAEC	small airway:	n/a
17	chr12:25347752-25347802	NHBE	bronchial:	n/a
18	chr12:25347752-25347802	K562	blood:	n/a
19	chr12:25347752-25347802	HL-60	blood:	n/a
20	chr12:25347752-25347802	ovcar-3	ovarian:	n/a
21	chr12:25347752-25347802	HEEpiC	esophagus:	n/a
22	chr12:25347752-25347802	GM12878	blood:	n/a
23	chr12:25347752-25347802	ProgFib	skin:	n/a
24	chr12:25347752-25347802	Hela-S3	cervix:	n/a
25	chr12:25347752-25347802	Jurkat	blood:	n/a
26	chr12:25347752-25347802	HepG2	liver:	n/a
27	chr12:25347752-25347802	HIPEpiC	eye:	n/a
28	chr12:25347752-25347802	SKMC	muscle:	n/a
29	chr12:25347752-25347802	HCPEpiC	choroid plexus:	n/a
30	chr12:25347752-25347802	SK-N-SH	brain:	n/a
31	chr12:25347752-25347802	HCT-116	colon:	n/a
32	chr12:25347752-25347802	BJ	skin:	n/a
33	chr12:25347752-25347802	PrEC	prostate:	n/a
34	chr12:25347752-25347802	ECC-1	luminal epithelium:	n/a
35	chr12:25347752-25347802	HCM	heart:	n/a
36	chr12:25347752-25347802	NT2-D1	testis:	n/a
37	chr12:25347752-25347802	HRPEpiC	eye:	n/a
38	chr12:25347752-25347802	NHDF-neo	bronchial:	n/a
39	chr12:25347752-25347802	PFSK-1	brain:	n/a
40	chr12:25347752-25347802	Hepatocyte	liver:	n/a
41	chr12:25347752-25347802	Caco-2	colon:	n/a
42	chr12:25347752-25347802	GM12891	blood:	n/a
43	chr12:25347752-25347802	SK-N-SH_RA	brain:	n/a
44	chr12:25347752-25347802	HEK293	kidney:	embryo
45	chr12:25347752-25347802	IMR90	lung:	fetal
46	chr12:25347752-25347802	SK-N-MC	brain:	n/a
47	chr12:25347752-25347802	AG09309	skin:	n/a
48	chr12:25347752-25347802	AoSMC	blood vessel:	n/a
49	chr12:25347752-25347802	CMK	blood:	n/a
50	chr12:25347752-25347802	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:25346543..25348618-chr12:25402303..25405258,3	K562	blood:
2	chr12:25346725..25349884-chr12:25402144..25405058,5	K562	blood:
3	chr12:25347765..25350303-chr12:25380801..25383112,2	K562	blood:

Variant related genes	Relation type
LYRM5	TF binding region
LYRM5	CpG island
ENSG00000268076	Chromatin interaction
ENSG00000133703	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs56031509	1.00[EUR][1000 genomes]
rs56156532	1.00[EUR][1000 genomes]
rs56225858	1.00[EUR][1000 genomes]
rs61762415	1.00[EUR][1000 genomes]
rs61762420	1.00[EUR][1000 genomes]
rs61764372	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73067299	1.00[EUR][1000 genomes]
rs73069109	1.00[EUR][1000 genomes]
rs73069133	1.00[EUR][1000 genomes]
rs73069144	1.00[EUR][1000 genomes]
rs73071282	1.00[EUR][1000 genomes]
rs73071287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73071296	1.00[EUR][1000 genomes]
rs73071297	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73071298	1.00[EUR][1000 genomes]
rs73071299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73081232	0.89[EUR][1000 genomes]
rs73081719	1.00[EUR][1000 genomes]
rs73081729	1.00[EUR][1000 genomes]
rs7308237	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25347200-25347800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:25347200-25347800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:25347200-25347800	Flanking Active TSS	Fetal Lung	lung
4	chr12:25347200-25348000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:25347200-25348600	Active TSS	Fetal Brain Female	brain
6	chr12:25347200-25349400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:25347400-25347800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr12:25347400-25347800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:25347400-25347800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:25347400-25347800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr12:25347400-25347800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr12:25347400-25347800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:25347400-25347800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:25347400-25347800	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr12:25347400-25347800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:25347400-25347800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr12:25347400-25347800	Flanking Active TSS	Fetal Heart	heart
18	chr12:25347400-25347800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr12:25347400-25347800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr12:25347400-25347800	Flanking Active TSS	A549	lung
21	chr12:25347400-25348000	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr12:25347400-25348000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr12:25347400-25348000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr12:25347400-25348000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr12:25347400-25348000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:25347400-25348000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:25347400-25348000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:25347400-25348000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr12:25347400-25348000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:25347400-25348000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:25347400-25348000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr12:25347400-25348000	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr12:25347400-25348000	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr12:25347400-25348000	ZNF genes & repeats	Fetal Brain Male	brain
35	chr12:25347400-25348000	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr12:25347400-25348000	Flanking Active TSS	Dnd41	blood
37	chr12:25347400-25348000	Flanking Active TSS	HMEC	breast
38	chr12:25347400-25348000	Flanking Active TSS	NHEK	skin
39	chr12:25347400-25348800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:25347400-25348800	Active TSS	Muscle Satellite Cultured Cells	--
41	chr12:25347400-25349000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:25347400-25349000	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr12:25347400-25349000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:25347400-25349000	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr12:25347400-25349000	Active TSS	Psoas Muscle	Psoas
46	chr12:25347400-25349000	Active TSS	NHDF-Ad	bronchial
47	chr12:25347400-25349200	Active TSS	Brain Angular Gyrus	brain
48	chr12:25347400-25349200	Active TSS	K562	blood
49	chr12:25347400-25349400	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr12:25347600-25347800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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