Variant report

Variant	rs12258923
Chromosome Location	chr10:112627878-112627879
allele	A/C
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	TBL1XR1	chr10:112627872-112627880	GM12878	blood:	n/a	n/a
2	STAT5A	chr10:112627182-112627970	GM12878	blood:	n/a	chr10:112627499-112627511
3	RCOR1	chr10:112627256-112627947	GM12878	blood:	n/a	n/a
4	SPI1	chr10:112626918-112628042	GM12878	blood:	n/a	chr10:112627482-112627495 chr10:112627676-112627683
5	POLR2A	chr10:112627210-112628314	GM12891	blood:	n/a	n/a
6	MTA3	chr10:112627110-112628318	GM12878	blood:	n/a	n/a
7	RUNX3	chr10:112627129-112627915	GM12878	blood:	n/a	n/a
8	RELA	chr10:112627240-112628036	GM19099	blood:	n/a	n/a
9	CHD2	chr10:112627872-112628042	GM12878	blood:	n/a	n/a
10	NFIC	chr10:112627131-112628229	GM12878	blood:	n/a	n/a
11	NFIC	chr10:112627181-112627993	GM12878	blood:	n/a	n/a
12	BCLAF1	chr10:112627194-112628196	GM12878	blood:	n/a	n/a
13	FOXM1	chr10:112627053-112628137	GM12878	blood:	n/a	n/a
14	MTA3	chr10:112627143-112628004	GM12878	blood:	n/a	n/a
15	PML	chr10:112627133-112628008	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:112541266..112543726-chr10:112626474..112628213,2	MCF-7	breast:
2	chr10:112626462..112628897-chr10:112630729..112632861,3	MCF-7	breast:
3	chr10:112566725..112569473-chr10:112626744..112628877,2	MCF-7	breast:
4	chr10:112361402..112363678-chr10:112626745..112629096,2	K562	blood:
5	chr10:112580755..112589346-chr10:112627817..112636075,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232470	TF binding region
PDCD4	TF binding region
ENSG00000203867	Chromatin interaction
ENSG00000150593	Chromatin interaction
ENSG00000203497	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11195357	1.00[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11195367	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11195378	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11195384	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11195386	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11195389	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11195392	0.88[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11195393	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12240492	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12244153	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12245003	0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap]
rs12248431	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12248632	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12248739	1.00[ASW][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12249906	0.88[YRI][hapmap]
rs12255335	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12256152	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12266042	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12267661	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12268160	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12268606	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1327552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1341055	0.87[ASW][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes]
rs1410052	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1538998	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17128099	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17128102	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17128270	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3750621	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3750622	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3763691	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4917593	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4918610	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55879225	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56005122	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56302131	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56350255	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9804245	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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
5	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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112611200-112630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:112617000-112628600	Enhancers	Placenta	Placenta
3	chr10:112617800-112630600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:112618400-112630800	Enhancers	Fetal Thymus	thymus
5	chr10:112621000-112630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:112621000-112631000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:112621200-112630400	Weak transcription	Gastric	stomach
8	chr10:112621200-112630600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:112621200-112630600	Weak transcription	Brain Substantia Nigra	brain
10	chr10:112621800-112628600	Enhancers	Fetal Muscle Leg	muscle
11	chr10:112622000-112628400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:112622200-112628400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr10:112623000-112630600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr10:112623200-112628200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr10:112623400-112631000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:112623800-112628400	Enhancers	Small Intestine	intestine
17	chr10:112624000-112630600	Weak transcription	Lung	lung
18	chr10:112624200-112628200	Enhancers	HSMM	muscle
19	chr10:112624400-112628400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr10:112624400-112628400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:112624400-112628600	Enhancers	Placenta Amnion	Placenta Amnion
22	chr10:112624800-112628800	Weak transcription	Dnd41	blood
23	chr10:112625000-112628600	Enhancers	Primary T cells fromperipheralblood	blood
24	chr10:112625000-112628800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr10:112625000-112628800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:112625000-112629200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr10:112625000-112629600	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr10:112625000-112630200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr10:112625000-112630800	Enhancers	Primary hematopoietic stem cells	blood
30	chr10:112625000-112631000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr10:112625200-112628200	Enhancers	HSMMtube	muscle
32	chr10:112625200-112630800	Enhancers	Thymus	Thymus
33	chr10:112625400-112628200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:112625400-112628200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr10:112625400-112628400	Enhancers	Colonic Mucosa	Colon
36	chr10:112625400-112628800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr10:112625400-112629400	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr10:112625400-112630000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:112625400-112630400	Weak transcription	Brain Anterior Caudate	brain
40	chr10:112625400-112630600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr10:112625400-112630600	Weak transcription	Brain Hippocampus Middle	brain
42	chr10:112625400-112630600	Enhancers	K562	blood
43	chr10:112625600-112628400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:112625600-112628600	Enhancers	Primary T cells from cord blood	blood
45	chr10:112625600-112628600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr10:112625600-112629000	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr10:112625600-112629000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr10:112625600-112630400	Weak transcription	Fetal Heart	heart
49	chr10:112625600-112630800	Weak transcription	NH-A	brain
50	chr10:112625800-112630400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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