Variant report

Variant	rs12219240
Chromosome Location	chr10:97051083-97051084
allele	C/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	HA-E2F1	chr10:97050172-97051493	MCF-7	breast:	n/a	chr10:97050800-97050810 chr10:97050499-97050508 chr10:97050829-97050839
2	CBX3	chr10:97051022-97051417	K562	blood:	n/a	n/a
3	MAZ	chr10:97048886-97051702	IMR90	lung:	n/a	chr10:97050825-97050835
4	SIN3AK20	chr10:97050869-97051136	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr10:97050542-97051337	A549	lung:	n/a	chr10:97050825-97050835
6	MXI1	chr10:97050269-97051268	GM12878	blood:	n/a	n/a
7	E2F6	chr10:97050295-97051504	A549	lung:	n/a	chr10:97051067-97051078 chr10:97050800-97050810 chr10:97050499-97050508 chr10:97050829-97050839
8	MAX	chr10:97050243-97051488	HepG2	liver:	n/a	chr10:97050825-97050835
9	CBX3	chr10:97050865-97051470	K562	blood:	n/a	n/a
10	YY1	chr10:97050238-97051204	GM12892	blood:	n/a	chr10:97050380-97050394 chr10:97050793-97050804 chr10:97050828-97050837
11	STAT5A	chr10:97050429-97052041	GM12878	blood:	n/a	n/a
12	E2F4	chr10:97050482-97051292	K562	blood:	n/a	chr10:97050800-97050810 chr10:97050499-97050508 chr10:97050829-97050839
13	E2F4	chr10:97050624-97051455	MCF10A-Er-Src	breast:	n/a	chr10:97050800-97050810 chr10:97050829-97050839
14	YY1	chr10:97050369-97051127	SK-N-SH	brain:	n/a	chr10:97050380-97050394 chr10:97050793-97050804 chr10:97050828-97050837
15	HCFC1	chr10:97051052-97051397	K562	blood:	n/a	n/a
16	EP300	chr10:97051042-97051112	HepG2	liver:	n/a	n/a
17	MAX	chr10:97050507-97051313	MCF-7	breast:	n/a	chr10:97050825-97050835
18	ZEB1	chr10:97050564-97051108	GM12878	blood:	n/a	n/a
19	E2F6	chr10:97050445-97051339	K562	blood:	n/a	chr10:97051067-97051078 chr10:97050800-97050810 chr10:97050499-97050508 chr10:97050829-97050839
20	MAX	chr10:97050147-97051499	ECC-1	luminal epithelium:	n/a	chr10:97050825-97050835
21	MYC	chr10:97050201-97051318	K562	blood:	n/a	chr10:97050825-97050835
22	ATF2	chr10:97050952-97051307	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr10:97050246-97051883	GM12878	blood:	n/a	n/a
24	STAT1	chr10:97050240-97051168	GM12878	blood:	n/a	n/a
25	POLR2A	chr10:97050149-97051146	ECC-1	luminal epithelium:	n/a	n/a
26	HDAC2	chr10:97050477-97051336	HepG2	liver:	n/a	n/a
27	CREB1	chr10:97050470-97051261	A549	lung:	n/a	n/a
28	POLR2A	chr10:97050464-97051136	K562	blood:	n/a	n/a
29	MAX	chr10:97049275-97051652	A549	lung:	n/a	chr10:97050825-97050835
30	POLR2A	chr10:97050135-97051155	A549	lung:	n/a	n/a
31	POLR2A	chr10:97050324-97051199	PANC-1	pancreas:	n/a	n/a
32	ZNF143	chr10:97050397-97051421	GM12878	blood:	n/a	chr10:97050800-97050810
33	TCF12	chr10:97049095-97051559	A549	lung:	n/a	chr10:97050095-97050102 chr10:97050563-97050573 chr10:97051071-97051081
34	POLR2A	chr10:97050196-97051213	GM18526	blood:	n/a	n/a
35	MEF2A	chr10:97050536-97051249	GM12878	blood:	n/a	n/a
36	MAX	chr10:97050372-97051416	MCF-7	breast:	n/a	chr10:97050825-97050835
37	RCOR1	chr10:97050708-97051457	K562	blood:	n/a	n/a
38	POLR2A	chr10:97050864-97051102	A549	lung:	n/a	n/a
39	RCOR1	chr10:97050503-97051469	K562	blood:	n/a	n/a
40	TBL1XR1	chr10:97050470-97051449	GM12878	blood:	n/a	n/a
41	ZNF143	chr10:97050904-97051432	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr10:97049406-97051133	MCF10A-Er-Src	breast:	n/a	n/a
43	E2F6	chr10:97050667-97051173	K562	blood:	n/a	chr10:97051067-97051078 chr10:97050800-97050810 chr10:97050829-97050839
44	BCLAF1	chr10:97050169-97051390	GM12878	blood:	n/a	chr10:97050499-97050512 chr10:97050356-97050369
45	PAX5	chr10:97050211-97051149	GM12892	blood:	n/a	chr10:97050356-97050365
46	POLR2A	chr10:97050145-97051135	K562	blood:	n/a	n/a
47	MAX	chr10:97050387-97051443	H1-hESC	embryonic stem cell:	n/a	chr10:97050825-97050835
48	POLR2A	chr10:97050192-97051925	GM12892	blood:	n/a	n/a
49	POLR2A	chr10:97050400-97051889	GM12892	blood:	n/a	n/a
50	TCF12	chr10:97050156-97051316	ECC-1	luminal epithelium:	n/a	chr10:97050563-97050573 chr10:97051071-97051081

No.	Distal block	Cell Line	Cell type
1	chr10:97050094..97051679-chr11:65189591..65191802,2	MCF-7	breast:
2	chr10:97031617..97033623-chr10:97049399..97051211,2	K562	blood:
3	chr10:97050804..97052725-chr10:97120124..97123059,2	K562	blood:
4	chr10:96989099..96991002-chr10:97047738..97051859,4	MCF-7	breast:
5	chr10:97002381..97008883-chr10:97045266..97052392,13	MCF-7	breast:
6	chr10:97030116..97038568-chr10:97046190..97052064,12	MCF-7	breast:
7	chr10:97050574..97051322-chr14:53258313..53259081,2	Hela-S3	cervix:

Variant related genes	Relation type
PDLIM1	TF binding region
ENSG00000234026	Chromatin interaction
ENSG00000100522	Chromatin interaction
ENSG00000107438	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10882577	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188257	0.93[ASN][1000 genomes]
rs11188258	0.95[ASN][1000 genomes]
rs11188259	0.95[ASN][1000 genomes]
rs11188260	0.95[ASN][1000 genomes]
rs11188262	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188263	0.95[ASN][1000 genomes]
rs11599160	0.89[EUR][1000 genomes]
rs12219257	0.99[ASN][1000 genomes]
rs6583989	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6583990	0.85[ASN][1000 genomes]
rs7921287	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 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	chr10:97047400-97051200	Active TSS	Aorta	Aorta
2	chr10:97048200-97051400	Active TSS	Rectal Smooth Muscle	rectum
3	chr10:97048400-97051200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr10:97049000-97051200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr10:97049000-97051400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:97049000-97051400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
7	chr10:97049000-97051400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr10:97049200-97051200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr10:97049200-97051200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr10:97049200-97051400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
11	chr10:97049200-97051400	Active TSS	NHEK	skin
12	chr10:97049400-97051200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr10:97049400-97051200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:97049400-97051200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:97049400-97051200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:97049400-97051200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:97049400-97051200	Active TSS	Right Ventricle	heart
18	chr10:97049400-97051400	Active TSS	Duodenum Mucosa	Duodenum
19	chr10:97049600-97051200	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr10:97049600-97051200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr10:97049600-97051200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
22	chr10:97049600-97051200	Active TSS	Esophagus	oesophagus
23	chr10:97049600-97051200	Active TSS	Fetal Kidney	kidney
24	chr10:97049600-97051200	Active TSS	Left Ventricle	heart
25	chr10:97049600-97051200	Active TSS	Ovary	ovary
26	chr10:97049600-97051200	Active TSS	Psoas Muscle	Psoas
27	chr10:97049600-97051400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr10:97049800-97051200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:97049800-97051200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr10:97049800-97051200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
31	chr10:97049800-97051200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr10:97049800-97051200	Active TSS	A549	lung
33	chr10:97049800-97051200	Active TSS	NHDF-Ad	bronchial
34	chr10:97049800-97051400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr10:97049800-97051400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr10:97049800-97051400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:97049800-97051400	Active TSS	HSMMtube	muscle
38	chr10:97049800-97051800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr10:97050000-97051200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:97050000-97051200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:97050000-97051200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr10:97050000-97051200	Active TSS	Primary B cells from cord blood	blood
43	chr10:97050000-97051200	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr10:97050000-97051200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:97050000-97051200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr10:97050000-97051200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
47	chr10:97050000-97051200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
48	chr10:97050000-97051200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
49	chr10:97050000-97051200	Bivalent/Poised TSS	Fetal Brain Female	brain
50	chr10:97050000-97051400	Active TSS	Skeletal Muscle Female	skeletal muscle

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