Variant report

Variant	rs56087058
Chromosome Location	chr10:43895321-43895322
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	POLR2A	chr10:43888984-43898060	K562	blood:	n/a	n/a
2	POLR2A	chr10:43894112-43895932	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:43894263-43895515	IMR90	lung:	n/a	n/a
4	WRNIP1	chr10:43894546-43895491	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:43890409-43895371	GM12892	blood:	n/a	n/a
6	TEAD4	chr10:43893980-43895520	K562	blood:	n/a	chr10:43895016-43895025
7	JUND	chr10:43894780-43895410	HepG2	liver:	n/a	chr10:43895204-43895212
8	POLR2A	chr10:43893253-43895533	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr10:43890420-43895659	GM12892	blood:	n/a	n/a
10	ARID3A	chr10:43894477-43895368	HepG2	liver:	n/a	n/a
11	POLR2A	chr10:43894070-43896282	HepG2	liver:	n/a	n/a
12	FOS	chr10:43894921-43895371	MCF10A-Er-Src	breast:	n/a	chr10:43895204-43895212
13	PBX3	chr10:43894786-43895434	SK-N-SH	brain:	n/a	n/a
14	FOS	chr10:43894961-43895350	MCF10A-Er-Src	breast:	n/a	chr10:43895204-43895212
15	POLR2A	chr10:43894150-43896238	K562	blood:	n/a	n/a
16	POLR2A	chr10:43894492-43895673	HL-60	blood:	n/a	n/a
17	POLR2A	chr10:43893291-43895398	GM12891	blood:	n/a	n/a
18	POLR2A	chr10:43894064-43898053	K562	blood:	n/a	n/a
19	POLR2A	chr10:43894690-43895422	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr10:43894450-43895568	HepG2	liver:	n/a	n/a
21	POLR2A	chr10:43894034-43895619	GM12878	blood:	n/a	n/a
22	JUN	chr10:43894781-43895389	HepG2	liver:	n/a	chr10:43895204-43895212
23	POLR2A	chr10:43878581-43905107	K562	blood:	n/a	n/a
24	POLR2A	chr10:43894005-43895326	GM12892	blood:	n/a	n/a
25	POLR2A	chr10:43894073-43895684	Hela-S3	cervix:	n/a	n/a
26	CEBPB	chr10:43894548-43895321	HCT-116	colon:	n/a	chr10:43894918-43894929 chr10:43894919-43894930 chr10:43894920-43894929
27	POLR2A	chr10:43894065-43895503	HL-60	blood:	n/a	n/a
28	GATA3	chr10:43894723-43895403	SK-N-SH	brain:	n/a	chr10:43895202-43895211
29	FOS	chr10:43894854-43895563	MCF10A-Er-Src	breast:	n/a	chr10:43895204-43895212 chr10:43895433-43895444
30	POLR2A	chr10:43893359-43895390	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr10:43893872-43895705	K562	blood:	n/a	n/a
32	POLR2A	chr10:43894170-43895379	GM12878	blood:	n/a	n/a
33	POLR2A	chr10:43895309-43895325	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr10:43894863-43895540	MCF-7	breast:	n/a	n/a
35	POLR2A	chr10:43893271-43895606	GM12892	blood:	n/a	n/a
36	POLR2A	chr10:43891015-43896319	K562	blood:	n/a	n/a
37	POLR2A	chr10:43888975-43895565	GM12891	blood:	n/a	n/a
38	POLR2A	chr10:43894993-43895354	U87	brain:	n/a	n/a
39	POLR2A	chr10:43894427-43895502	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr10:43894101-43899596	HepG2	liver:	n/a	n/a
41	POLR2A	chr10:43893317-43895466	GM12878	blood:	n/a	n/a
42	POLR2A	chr10:43893441-43899649	A549	lung:	n/a	n/a
43	POLR2A	chr10:43893295-43895595	GM12891	blood:	n/a	n/a
44	PML	chr10:43894101-43895732	K562	blood:	n/a	chr10:43894287-43894295 chr10:43895205-43895214
45	POLR2A	chr10:43893330-43895389	GM12891	blood:	n/a	n/a
46	FOS	chr10:43894807-43895383	MCF10A-Er-Src	breast:	n/a	chr10:43895204-43895212
47	GATA3	chr10:43894734-43895461	SK-N-SH	brain:	n/a	chr10:43895202-43895211
48	TEAD4	chr10:43894649-43895392	HepG2	liver:	n/a	chr10:43895016-43895025
49	POLR2A	chr10:43886840-43895529	K562	blood:	n/a	n/a
50	JUND	chr10:43894173-43895378	K562	blood:	n/a	chr10:43895204-43895212

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43887055..43906178-chr10:43946385..43955803,85	K562	blood:

Variant related genes	Relation type
HNRNPF	TF binding region
ENSG00000252532	Chromatin interaction
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1106215	1.00[ASN][1000 genomes]
rs11238575	1.00[ASN][1000 genomes]
rs17153601	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17366781	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856400	1.00[ASN][1000 genomes]
rs1879311	1.00[ASN][1000 genomes]
rs2248707	0.85[AFR][1000 genomes]
rs2248807	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253260	1.00[ASN][1000 genomes]
rs2261637	0.85[EUR][1000 genomes]
rs2264603	1.00[ASN][1000 genomes]
rs2265955	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812798	0.91[EUR][1000 genomes]
rs2819025	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999222	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999288	0.85[EUR][1000 genomes]
rs2999290	0.85[EUR][1000 genomes]
rs3006393	1.00[ASN][1000 genomes]
rs3006410	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3124211	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948727	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55765722	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56037308	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234785	1.00[ASN][1000 genomes]
rs56237566	1.00[ASN][1000 genomes]
rs56252639	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56275379	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072967	1.00[ASN][1000 genomes]
rs7073345	1.00[ASN][1000 genomes]
rs7084621	1.00[ASN][1000 genomes]
rs7085670	1.00[ASN][1000 genomes]
rs72785234	1.00[ASN][1000 genomes]
rs72785236	1.00[ASN][1000 genomes]
rs72785237	1.00[ASN][1000 genomes]
rs72785243	1.00[ASN][1000 genomes]
rs72785246	1.00[ASN][1000 genomes]
rs72785248	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785255	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785256	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785266	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787434	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916718	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9422365	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825355	chr10:43890579-43923802	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 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	chr10:43892200-43896600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:43893000-43895400	Enhancers	Pancreas	Pancrea
3	chr10:43893000-43895600	Enhancers	Spleen	Spleen
4	chr10:43893000-43897000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:43893200-43895400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr10:43893200-43895400	Flanking Active TSS	Liver	Liver
7	chr10:43893200-43895600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:43893200-43895600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr10:43893200-43895600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:43893200-43895600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr10:43893200-43895600	Enhancers	Small Intestine	intestine
12	chr10:43893200-43898400	Genic enhancers	Hela-S3	cervix
13	chr10:43893200-43901600	Weak transcription	HSMMtube	muscle
14	chr10:43893400-43895600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr10:43893400-43895600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:43893400-43895600	Enhancers	Psoas Muscle	Psoas
17	chr10:43893400-43896200	Transcr. at gene 5' and 3'	Dnd41	blood
18	chr10:43893400-43899800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
19	chr10:43893400-43901400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr10:43893600-43895600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr10:43893600-43895600	Enhancers	Thymus	Thymus
22	chr10:43893600-43897000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr10:43893600-43899000	Enhancers	HUVEC	blood vessel
24	chr10:43893600-43899800	Genic enhancers	NHEK	skin
25	chr10:43893600-43901200	Weak transcription	Brain Angular Gyrus	brain
26	chr10:43893600-43902200	Weak transcription	Aorta	Aorta
27	chr10:43893800-43895600	Enhancers	Gastric	stomach
28	chr10:43893800-43895800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr10:43893800-43897400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr10:43893800-43897400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr10:43893800-43897400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
32	chr10:43893800-43898400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr10:43893800-43898800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:43893800-43899000	Weak transcription	Brain Substantia Nigra	brain
35	chr10:43894000-43895400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:43894000-43895800	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr10:43894000-43899400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:43894000-43899800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:43894000-43901200	Weak transcription	Brain Hippocampus Middle	brain
40	chr10:43894000-43901200	Genic enhancers	Fetal Intestine Small	intestine
41	chr10:43894000-43901400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr10:43894200-43895400	Genic enhancers	Primary B cells from cord blood	blood
43	chr10:43894200-43895400	Genic enhancers	Fetal Heart	heart
44	chr10:43894200-43895600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr10:43894200-43895600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr10:43894200-43895800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr10:43894200-43896000	Genic enhancers	Osteobl	bone
48	chr10:43894200-43897400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:43894200-43899200	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr10:43894200-43899200	Transcr. at gene 5' and 3'	K562	blood

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