Variant report

Variant	rs12258559
Chromosome Location	chr10:112633172-112633173
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	chr10:112630523-112633327	GM18505	blood:	n/a	n/a
2	EP300	chr10:112631987-112633226	K562	blood:	n/a	chr10:112632369-112632385
3	TBP	chr10:112630608-112633283	K562	blood:	n/a	n/a
4	TBL1XR1	chr10:112632439-112633478	K562	blood:	n/a	n/a
5	POLR2A	chr10:112631220-112633272	IMR90	lung:	n/a	n/a
6	POLR2A	chr10:112631213-112633499	MCF10A-Er-Src	breast:	n/a	n/a
7	CHD1	chr10:112630906-112633586	GM12878	blood:	n/a	chr10:112632208-112632218 chr10:112632079-112632089
8	POLR2A	chr10:112630530-112633327	GM19099	blood:	n/a	n/a
9	MYC	chr10:112631950-112633317	MCF10A-Er-Src	breast:	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
10	POLR2A	chr10:112631177-112633314	K562	blood:	n/a	n/a
11	POLR2A	chr10:112631864-112633317	GM12878	blood:	n/a	n/a
12	STAT3	chr10:112632469-112633229	MCF10A-Er-Src	breast:	n/a	chr10:112632821-112632832
13	MXI1	chr10:112630386-112634137	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr10:112631096-112633615	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr10:112630610-112633472	PBDE	blood:	n/a	n/a
16	MXI1	chr10:112633144-112633747	GM12878	blood:	n/a	n/a
17	ARID3A	chr10:112632088-112633228	HepG2	liver:	n/a	n/a
18	POLR2A	chr10:112630627-112634252	GM12878	blood:	n/a	n/a
19	MXI1	chr10:112630929-112634169	IMR90	lung:	n/a	n/a
20	POLR2A	chr10:112631717-112633195	A549	lung:	n/a	n/a
21	ARID3A	chr10:112632512-112633670	K562	blood:	n/a	n/a
22	RFX5	chr10:112630240-112633396	SK-N-SH	brain:	n/a	n/a
23	CHD1	chr10:112630625-112634072	IMR90	lung:	n/a	chr10:112632208-112632218 chr10:112632079-112632089
24	TBP	chr10:112632472-112633276	GM12878	blood:	n/a	n/a
25	POLR2A	chr10:112630408-112633274	GM12878	blood:	n/a	n/a
26	RFX5	chr10:112630567-112633448	IMR90	lung:	n/a	n/a
27	POLR2A	chr10:112629899-112634013	GM12891	blood:	n/a	n/a
28	FOXM1	chr10:112632324-112633177	GM12878	blood:	n/a	n/a
29	MAZ	chr10:112631061-112633320	IMR90	lung:	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
30	POLR2A	chr10:112632966-112633193	GM12891	blood:	n/a	n/a
31	TBP	chr10:112632458-112633562	Hela-S3	cervix:	n/a	n/a
32	MYC	chr10:112632355-112633408	MCF10A-Er-Src	breast:	n/a	chr10:112632424-112632431 chr10:112632814-112632822 chr10:112632423-112632434 chr10:112632422-112632435 chr10:112632424-112632433 chr10:112632423-112632434
33	MAX	chr10:112633134-112633844	Hela-S3	cervix:	n/a	n/a
34	EP300	chr10:112632510-112633247	GM12878	blood:	n/a	n/a
35	EP300	chr10:112632509-112633407	Hela-S3	cervix:	n/a	n/a
36	SIN3A	chr10:112633062-112633203	GM12878	blood:	n/a	n/a
37	POLR2A	chr10:112630864-112637039	MCF10A-Er-Src	breast:	n/a	n/a
38	ZNF143	chr10:112633034-112633200	GM12878	blood:	n/a	n/a

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	chr10:112632404..112635995-chr10:112677494..112680497,3	MCF-7	breast:
4	chr10:112327690..112330485-chr10:112631078..112633307,2	K562	blood:
5	chr10:112630522..112633740-chr10:112677502..112680452,8	K562	blood:
6	chr10:112630933..112635987-chr10:112638238..112642004,12	MCF-7	breast:
7	chr10:112506327..112507861-chr10:112632339..112634018,2	MCF-7	breast:
8	chr10:112632441..112634715-chr8:128746659..128749011,2	MCF-7	breast:
9	chr10:112581444..112587243-chr10:112629842..112633404,6	MCF-7	breast:
10	chr10:112580755..112589346-chr10:112627817..112636075,27	MCF-7	breast:
11	chr10:112485811..112488574-chr10:112632571..112634625,2	MCF-7	breast:
12	chr10:112630166..112634091-chr10:112649118..112655902,7	MCF-7	breast:
13	chr10:112563889..112566843-chr10:112632108..112634836,3	MCF-7	breast:
14	chr10:112593951..112595858-chr10:112632498..112635240,2	MCF-7	breast:

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

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10787286	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10885059	0.84[ASN][1000 genomes]
rs10885060	0.84[ASN][1000 genomes]
rs10885073	0.81[AFR][1000 genomes]
rs11195361	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11195366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11195391	0.81[AFR][1000 genomes]
rs12240685	0.88[AFR][1000 genomes]
rs12253351	0.81[AFR][1000 genomes]
rs12261765	0.88[AFR][1000 genomes]
rs2146544	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34401279	0.86[AFR][1000 genomes]
rs35394459	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs35946882	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3763692	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7089687	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7919142	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][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:126 , 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	chr10:112631200-112633200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr10:112631200-112633200	Active TSS	Fetal Kidney	kidney
10	chr10:112631200-112633200	Active TSS	Gastric	stomach
11	chr10:112631200-112633400	Active TSS	Brain Angular Gyrus	brain
12	chr10:112631200-112633400	Active TSS	Placenta Amnion	Placenta Amnion
13	chr10:112631200-112633600	Active TSS	Brain Substantia Nigra	brain
14	chr10:112631200-112633800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr10:112631200-112633800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:112631200-112633800	Active TSS	Small Intestine	intestine
17	chr10:112631200-112634000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:112631200-112634000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:112631200-112634000	Active TSS	Brain Hippocampus Middle	brain
20	chr10:112631200-112634000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:112631200-112634000	Active TSS	Right Ventricle	heart
22	chr10:112631200-112634000	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr10:112631200-112634000	Active TSS	Thymus	Thymus
24	chr10:112631200-112634000	Active TSS	HSMM	muscle
25	chr10:112631200-112634200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr10:112631200-112634200	Active TSS	Colonic Mucosa	Colon
27	chr10:112631200-112634600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:112631200-112634600	Active TSS	Colon Smooth Muscle	Colon
29	chr10:112631200-112634600	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr10:112631200-112634800	Active TSS	Fetal Brain Female	brain
31	chr10:112631200-112634800	Active TSS	Ovary	ovary
32	chr10:112631200-112635000	Active TSS	Duodenum Mucosa	Duodenum
33	chr10:112631400-112633200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:112631400-112633200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr10:112631400-112633200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr10:112631400-112633200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr10:112631400-112633200	Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr10:112631400-112633200	Active TSS	Brain Cingulate Gyrus	brain
39	chr10:112631400-112633200	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr10:112631400-112633400	Active TSS	H1 Cell Line	embryonic stem cell
41	chr10:112631400-112633400	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr10:112631400-112633400	Active TSS	Dnd41	blood
43	chr10:112631400-112633600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr10:112631400-112633600	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr10:112631400-112633600	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr10:112631400-112633600	Active TSS	Primary monocytes fromperipheralblood	blood
47	chr10:112631400-112633600	Active TSS	Primary T cells from cord blood	blood
48	chr10:112631400-112633600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:112631400-112633600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:112631400-112633600	Active TSS	Cortex derived primary cultured neurospheres	brain

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