Variant report

Variant	rs12219468
Chromosome Location	chr10:112632469-112632470
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	GABPA	chr10:112631897-112632684	A549	lung:	n/a	chr10:112632210-112632219
2	BRCA1	chr10:112632397-112632928	Hela-S3	cervix:	n/a	n/a
3	TAF1	chr10:112632199-112632473	HepG2	liver:	n/a	n/a
4	CTCF	chr10:112632400-112632550	GM12874	blood:	n/a	n/a
5	TAF7	chr10:112631567-112632515	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr10:112630984-112632518	ECC-1	luminal epithelium:	n/a	n/a
7	CTCFL	chr10:112632467-112632643	K562	blood:	n/a	n/a
8	EP300	chr10:112631217-112632754	SK-N-SH_RA	brain:	n/a	chr10:112632369-112632385
9	GABPA	chr10:112631867-112632519	MCF-7	breast:	n/a	chr10:112632210-112632219
10	USF1	chr10:112632176-112632852	ECC-1	luminal epithelium:	n/a	chr10:112632422-112632433 chr10:112632342-112632358
11	TCF7L2	chr10:112632059-112632761	PANC-1	pancreas:	n/a	n/a
12	CTCF	chr10:112632340-112632490	GM12866	blood:	n/a	chr10:112632346-112632359
13	SMC3	chr10:112630974-112632858	Hela-S3	cervix:	n/a	chr10:112632212-112632222
14	CTCF	chr10:112632380-112632530	GM12865	blood:	n/a	n/a
15	CEBPB	chr10:112632384-112632887	K562	blood:	n/a	n/a
16	TCF12	chr10:112631047-112632763	ECC-1	luminal epithelium:	n/a	n/a
17	SIN3AK20	chr10:112632196-112632698	H1-hESC	embryonic stem cell:	n/a	n/a
18	UBTF	chr10:112631531-112632811	K562	blood:	n/a	n/a
19	POLR2A	chr10:112631877-112632603	PANC-1	pancreas:	n/a	n/a
20	SIN3AK20	chr10:112631351-112632809	SK-N-SH	brain:	n/a	n/a
21	RFX5	chr10:112631062-112632976	Hela-S3	cervix:	n/a	n/a
22	EP300	chr10:112632373-112632723	HepG2	liver:	n/a	n/a
23	CTCF	chr10:112632440-112632590	GM12872	blood:	n/a	n/a
24	TAF1	chr10:112631114-112632815	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr10:112631092-112632824	HepG2	liver:	n/a	n/a
26	SIN3AK20	chr10:112631866-112632725	K562	blood:	n/a	n/a
27	MAX	chr10:112631178-112632925	GM12878	blood:	n/a	chr10:112632424-112632431 chr10:112632814-112632822 chr10:112632041-112632051 chr10:112632423-112632434 chr10:112632422-112632435 chr10:112632424-112632433 chr10:112632423-112632434 chr10:112632275-112632285
28	POLR2A	chr10:112631153-112632826	K562	blood:	n/a	n/a
29	ZNF263	chr10:112630575-112632800	HEK293-T-REx	kidney:	n/a	chr10:112632115-112632124
30	MAX	chr10:112631166-112632842	H1-hESC	embryonic stem cell:	n/a	chr10:112632424-112632431 chr10:112632814-112632822 chr10:112632041-112632051 chr10:112632423-112632434 chr10:112632422-112632435 chr10:112632424-112632433 chr10:112632423-112632434 chr10:112632275-112632285
31	CTCF	chr10:112632380-112632530	A549	lung:	n/a	n/a
32	SIN3AK20	chr10:112632362-112632758	A549	lung:	n/a	n/a
33	POLR2A	chr10:112631121-112632744	GM12878	blood:	n/a	n/a
34	POLR2A	chr10:112630523-112633327	GM18505	blood:	n/a	n/a
35	POLR2A	chr10:112631095-112632760	H1-hESC	embryonic stem cell:	n/a	n/a
36	EP300	chr10:112631987-112633226	K562	blood:	n/a	chr10:112632369-112632385
37	MYC	chr10:112631969-112632752	K562	blood:	n/a	chr10:112632424-112632431 chr10:112632041-112632051 chr10:112632423-112632434 chr10:112632422-112632435 chr10:112632424-112632433 chr10:112632423-112632434 chr10:112632275-112632285
38	NFATC1	chr10:112631856-112632965	GM12878	blood:	n/a	n/a
39	SP1	chr10:112631060-112632791	A549	lung:	n/a	chr10:112632378-112632390 chr10:112632293-112632307 chr10:112632040-112632049 chr10:112632038-112632050 chr10:112632653-112632665 chr10:112631427-112631437 chr10:112632210-112632219 chr10:112632380-112632389 chr10:112632209-112632223 chr10:112632655-112632664 chr10:112632653-112632665 chr10:112632654-112632668 chr10:112632209-112632218 chr10:112632208-112632220 chr10:112632209-112632218 chr10:112631609-112631630 chr10:112632038-112632050 chr10:112632208-112632220 chr10:112632378-112632390 chr10:112631518-112631527 chr10:112632039-112632048
40	CTCF	chr10:112632440-112632590	NHEK	skin:	n/a	n/a
41	E2F6	chr10:112631879-112632712	K562	blood:	n/a	chr10:112632207-112632219 chr10:112632040-112632049 chr10:112632431-112632440 chr10:112632210-112632219
42	TBP	chr10:112630608-112633283	K562	blood:	n/a	n/a
43	POLR2A	chr10:112631099-112632707	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr10:112632380-112632530	HFF	foreskin:	n/a	n/a
45	TBL1XR1	chr10:112632439-112633478	K562	blood:	n/a	n/a
46	BACH1	chr10:112632032-112632586	H1-hESC	embryonic stem cell:	n/a	n/a
47	SIN3AK20	chr10:112630879-112633003	MCF-7	breast:	n/a	n/a
48	POLR2A	chr10:112630852-112633006	HL-60	blood:	n/a	n/a
49	RAD21	chr10:112631889-112632757	SK-N-SH_RA	brain:	n/a	chr10:112632212-112632222
50	MYC	chr10:112632394-112632674	Hela-S3	cervix:	n/a	chr10:112632424-112632431 chr10:112632423-112632434 chr10:112632422-112632435 chr10:112632424-112632433 chr10:112632423-112632434

No.	Distal block	Cell Line	Cell type
1	chr10:112631001..112634625-chr10:112648231..112651298,3	MCF-7	breast:
2	chr10:112630838..112635784-chr10:112676837..112681433,10	K562	blood:
3	chr10:112586696..112589138-chr10:112631404..112633158,2	K562	blood:
4	chr10:112632404..112635995-chr10:112677494..112680497,3	MCF-7	breast:
5	chr1:35658674..35659414-chr10:112632160..112632664,3	Hela-S3	cervix:
6	chr10:112327690..112330485-chr10:112631078..112633307,2	K562	blood:
7	chr10:112630522..112633740-chr10:112677502..112680452,8	K562	blood:
8	chr10:112630933..112635987-chr10:112638238..112642004,12	MCF-7	breast:
9	chr10:112632158..112632694-chr6:42896352..42896890,2	Hela-S3	cervix:
10	chr10:112506327..112507861-chr10:112632339..112634018,2	MCF-7	breast:
11	chr10:112632441..112634715-chr8:128746659..128749011,2	MCF-7	breast:
12	chr10:112581444..112587243-chr10:112629842..112633404,6	MCF-7	breast:
13	chr10:112580755..112589346-chr10:112627817..112636075,27	MCF-7	breast:
14	chr10:112630166..112634091-chr10:112649118..112655902,7	MCF-7	breast:
15	chr10:112563889..112566843-chr10:112632108..112634836,3	MCF-7	breast:

Variant related genes	Relation type
PDCD4-AS1	TF binding region
ENSG00000203867	Chromatin interaction
ENSG00000214413	Chromatin interaction
ENSG00000108055	Chromatin interaction
ENSG00000150593	Chromatin interaction
ENSG00000116560	Chromatin interaction
ENSG00000136997	Chromatin interaction
ENSG00000108061	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10787288	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10885062	0.82[AMR][1000 genomes]
rs11195360	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1327549	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1407696	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][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	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 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	chr10:112631000-112633200	Active TSS	Esophagus	oesophagus
2	chr10:112631000-112633200	Active TSS	Left Ventricle	heart
3	chr10:112631000-112633200	Active TSS	Pancreas	Pancrea
4	chr10:112631000-112633800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr10:112631000-112634000	Active TSS	Aorta	Aorta
6	chr10:112631000-112634000	Active TSS	Psoas Muscle	Psoas
7	chr10:112631000-112634200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:112631200-112632600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:112631200-112632800	Active TSS	Lung	lung
10	chr10:112631200-112632800	Active TSS	Spleen	Spleen
11	chr10:112631200-112633000	Active TSS	Brain Anterior Caudate	brain
12	chr10:112631200-112633200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr10:112631200-112633200	Active TSS	Fetal Kidney	kidney
14	chr10:112631200-112633200	Active TSS	Gastric	stomach
15	chr10:112631200-112633400	Active TSS	Brain Angular Gyrus	brain
16	chr10:112631200-112633400	Active TSS	Placenta Amnion	Placenta Amnion
17	chr10:112631200-112633600	Active TSS	Brain Substantia Nigra	brain
18	chr10:112631200-112633800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr10:112631200-112633800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr10:112631200-112633800	Active TSS	Small Intestine	intestine
21	chr10:112631200-112634000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:112631200-112634000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr10:112631200-112634000	Active TSS	Brain Hippocampus Middle	brain
24	chr10:112631200-112634000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:112631200-112634000	Active TSS	Right Ventricle	heart
26	chr10:112631200-112634000	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr10:112631200-112634000	Active TSS	Thymus	Thymus
28	chr10:112631200-112634000	Active TSS	HSMM	muscle
29	chr10:112631200-112634200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr10:112631200-112634200	Active TSS	Colonic Mucosa	Colon
31	chr10:112631200-112634600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:112631200-112634600	Active TSS	Colon Smooth Muscle	Colon
33	chr10:112631200-112634600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr10:112631200-112634800	Active TSS	Fetal Brain Female	brain
35	chr10:112631200-112634800	Active TSS	Ovary	ovary
36	chr10:112631200-112635000	Active TSS	Duodenum Mucosa	Duodenum
37	chr10:112631400-112632600	Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr10:112631400-112632600	Weak transcription	Fetal Heart	heart
39	chr10:112631400-112632600	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr10:112631400-112632800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr10:112631400-112632800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr10:112631400-112632800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:112631400-112633000	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr10:112631400-112633000	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr10:112631400-112633000	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr10:112631400-112633000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr10:112631400-112633200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr10:112631400-112633200	Active TSS	H9 Cell Line	embryonic stem cell
49	chr10:112631400-112633200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:112631400-112633200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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