Variant report

Variant	rs61732541
Chromosome Location	chr12:25347959-25347960
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	HMGN3	chr12:25347931-25348759	K562	blood:	n/a	n/a
2	SIN3AK20	chr12:25347837-25348171	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr12:25347216-25349605	SK-N-SH	brain:	n/a	chr12:25348081-25348096
4	POLR2A	chr12:25347861-25348663	GM12878	blood:	n/a	n/a
5	JUND	chr12:25347899-25348494	A549	lung:	n/a	n/a
6	POLR2A	chr12:25347504-25348981	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:25347957-25348851	H1-hESC	embryonic stem cell:	n/a	n/a
8	RCOR1	chr12:25347923-25348647	HepG2	liver:	n/a	n/a
9	FOXM1	chr12:25347744-25348767	GM12878	blood:	n/a	n/a
10	CTCF	chr12:25347959-25348689	K562	blood:	n/a	chr12:25348515-25348524
11	YY1	chr12:25347846-25348303	SK-N-SH_RA	brain:	n/a	chr12:25348158-25348167
12	EGR1	chr12:25347947-25348309	K562	blood:	n/a	chr12:25348157-25348167 chr12:25348097-25348107
13	POLR2A	chr12:25347826-25348658	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr12:25347803-25348709	HL-60	blood:	n/a	n/a
15	ELF1	chr12:25347859-25348692	GM12878	blood:	n/a	chr12:25348284-25348293
16	POLR2A	chr12:25347800-25348551	ProgFib	skin:	n/a	n/a
17	BCL3	chr12:25347759-25348635	A549	lung:	n/a	chr12:25348126-25348139
18	RUNX3	chr12:25347939-25348952	GM12878	blood:	n/a	chr12:25348502-25348511 chr12:25348502-25348511 chr12:25348240-25348257
19	MAX	chr12:25347873-25348622	GM12878	blood:	n/a	chr12:25348097-25348107
20	GABPA	chr12:25347912-25348341	K562	blood:	n/a	chr12:25348098-25348107 chr12:25348158-25348167
21	GABPA	chr12:25347875-25348486	SK-N-SH	brain:	n/a	chr12:25348098-25348107 chr12:25348158-25348167
22	SIN3AK20	chr12:25347883-25348587	K562	blood:	n/a	n/a
23	ELF1	chr12:25347807-25348589	GM12878	blood:	n/a	chr12:25348284-25348293
24	ELF1	chr12:25347855-25348575	MCF-7	breast:	n/a	chr12:25348284-25348293
25	SIN3AK20	chr12:25347853-25348595	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr12:25347927-25348520	Gliobla	brain:	n/a	n/a
27	MAX	chr12:25347800-25348746	ECC-1	luminal epithelium:	n/a	chr12:25348097-25348107
28	MAX	chr12:25347943-25348661	K562	blood:	n/a	chr12:25348097-25348107
29	TBP	chr12:25347826-25349005	K562	blood:	n/a	n/a
30	MAX	chr12:25347923-25348588	HepG2	liver:	n/a	chr12:25348097-25348107
31	HCFC1	chr12:25347139-25349028	Hela-S3	cervix:	n/a	n/a
32	EP300	chr12:25347949-25349040	GM12878	blood:	n/a	chr12:25348282-25348291 chr12:25348251-25348267 chr12:25348624-25348634
33	POLR2A	chr12:25347834-25348646	GM19193	blood:	n/a	n/a
34	POLR2A	chr12:25347727-25349494	PBDE	blood:	n/a	n/a
35	RCOR1	chr12:25347816-25348632	K562	blood:	n/a	n/a
36	POLR2A	chr12:25347870-25348622	HCT-116	colon:	n/a	n/a
37	MAX	chr12:25347926-25348743	A549	lung:	n/a	chr12:25348097-25348107
38	SIN3AK20	chr12:25347638-25348659	MCF-7	breast:	n/a	n/a
39	POLR2A	chr12:25347874-25349201	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:25347862-25348643	U87	brain:	n/a	n/a
41	ZNF143	chr12:25347915-25348680	H1-hESC	embryonic stem cell:	n/a	chr12:25348313-25348331
42	POLR2A	chr12:25347843-25348680	K562	blood:	n/a	n/a
43	REST	chr12:25347724-25349021	H1-neurons	neurons:	n/a	chr12:25348109-25348127
44	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
45	SIN3A	chr12:25347727-25348885	H1-hESC	embryonic stem cell:	n/a	n/a
46	SP4	chr12:25347911-25348301	H1-hESC	embryonic stem cell:	n/a	chr12:25348154-25348170 chr12:25348094-25348110 chr12:25348156-25348172 chr12:25348096-25348112
47	CHD2	chr12:25347789-25348733	K562	blood:	n/a	chr12:25348156-25348166
48	TAF1	chr12:25347815-25348666	K562	blood:	n/a	n/a
49	EGR1	chr12:25347947-25348298	K562	blood:	n/a	chr12:25348157-25348167 chr12:25348097-25348107
50	POLR2A	chr12:25347937-25348537	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:25346543..25348618-chr12:25402303..25405258,3	K562	blood:
2	chr10:93683014..93683556-chr12:25347907..25348654,2	NB4	blood:
3	chr12:25346725..25349884-chr12:25402144..25405058,5	K562	blood:
4	chr12:25347765..25350303-chr12:25380801..25383112,2	K562	blood:

Variant related genes	Relation type
LYRM5	TF binding region
ENSG00000268076	Chromatin interaction
ENSG00000095564	Chromatin interaction
ENSG00000133703	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16928546	0.92[AFR][1000 genomes]
rs16928548	0.95[AFR][1000 genomes]
rs16928568	0.95[AFR][1000 genomes]
rs56706074	1.00[AFR][1000 genomes]
rs59092193	0.95[AFR][1000 genomes]
rs61158742	1.00[AFR][1000 genomes]
rs61401861	1.00[AFR][1000 genomes]
rs61759628	0.95[AFR][1000 genomes]
rs61761095	0.95[AFR][1000 genomes]
rs61761153	0.95[AFR][1000 genomes]
rs61762419	0.90[AFR][1000 genomes]
rs61762425	1.00[AFR][1000 genomes]
rs61763585	1.00[AFR][1000 genomes]
rs73286885	1.00[AFR][1000 genomes]
rs73286888	1.00[AFR][1000 genomes]
rs73286892	1.00[AFR][1000 genomes]
rs73288812	0.95[AFR][1000 genomes]
rs73288817	1.00[AFR][1000 genomes]
rs73288818	1.00[AFR][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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25347200-25348000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:25347200-25348600	Active TSS	Fetal Brain Female	brain
3	chr12:25347200-25349400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:25347400-25348000	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr12:25347400-25348000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr12:25347400-25348000	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr12:25347400-25348000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr12:25347400-25348000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:25347400-25348000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:25347400-25348000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr12:25347400-25348000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr12:25347400-25348000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:25347400-25348000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:25347400-25348000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr12:25347400-25348000	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr12:25347400-25348000	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr12:25347400-25348000	ZNF genes & repeats	Fetal Brain Male	brain
18	chr12:25347400-25348000	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr12:25347400-25348000	Flanking Active TSS	Dnd41	blood
20	chr12:25347400-25348000	Flanking Active TSS	HMEC	breast
21	chr12:25347400-25348000	Flanking Active TSS	NHEK	skin
22	chr12:25347400-25348800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:25347400-25348800	Active TSS	Muscle Satellite Cultured Cells	--
24	chr12:25347400-25349000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:25347400-25349000	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr12:25347400-25349000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:25347400-25349000	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr12:25347400-25349000	Active TSS	Psoas Muscle	Psoas
29	chr12:25347400-25349000	Active TSS	NHDF-Ad	bronchial
30	chr12:25347400-25349200	Active TSS	Brain Angular Gyrus	brain
31	chr12:25347400-25349200	Active TSS	K562	blood
32	chr12:25347400-25349400	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr12:25347600-25348000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:25347600-25348000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr12:25347600-25348000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr12:25347600-25348000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr12:25347600-25348000	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr12:25347600-25348000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:25347600-25348000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:25347600-25348000	Flanking Active TSS	Liver	Liver
41	chr12:25347600-25348000	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr12:25347600-25348000	Flanking Active TSS	Placenta	Placenta
43	chr12:25347600-25348000	Flanking Active TSS	Fetal Thymus	thymus
44	chr12:25347600-25348000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr12:25347600-25348000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr12:25347600-25348000	Flanking Active TSS	GM12878-XiMat	blood
47	chr12:25347600-25348000	Flanking Active TSS	Hela-S3	cervix
48	chr12:25347600-25348000	Flanking Active TSS	HSMM	muscle
49	chr12:25347600-25348000	Flanking Active TSS	HSMMtube	muscle
50	chr12:25347600-25348000	Flanking Active TSS	HUVEC	blood vessel

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