Variant report

Variant	rs56121791
Chromosome Location	chr10:6182796-6182797
allele	C/T
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	NFIC	chr10:6182771-6184235	GM12878	blood:	n/a	n/a
2	FOXM1	chr10:6182764-6184342	GM12878	blood:	n/a	n/a
3	CUX1	chr10:6182685-6182833	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:6182780-6184101	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:6182336-6182945	GM12878	blood:	n/a	n/a
6	CHD1	chr10:6182777-6184233	IMR90	lung:	n/a	n/a
7	EBF1	chr10:6182473-6184172	GM12878	blood:	n/a	n/a
8	CHD1	chr10:6182327-6184009	GM12878	blood:	n/a	n/a
9	IKZF1	chr10:6182317-6184632	GM12878	blood:	n/a	n/a
10	MAZ	chr10:6182597-6184110	GM12878	blood:	n/a	n/a
11	RUNX3	chr10:6182401-6184334	GM12878	blood:	n/a	chr10:6183700-6183709
12	RUNX3	chr10:6182319-6184374	GM12878	blood:	n/a	chr10:6183700-6183709
13	CHD2	chr10:6182498-6184022	GM12878	blood:	n/a	n/a
14	EP300	chr10:6182517-6182823	GM12878	blood:	n/a	n/a
15	SPI1	chr10:6182514-6184066	GM12878	blood:	n/a	n/a
16	BHLHE40	chr10:6182477-6184159	GM12878	blood:	n/a	n/a
17	MAX	chr10:6182513-6184037	GM12878	blood:	n/a	n/a
18	EP300	chr10:6182404-6184252	GM12878	blood:	n/a	chr10:6182450-6182460
19	EBF1	chr10:6182511-6184195	GM12878	blood:	n/a	n/a
20	ELF1	chr10:6182101-6182921	GM12878	blood:	n/a	chr10:6182623-6182632
21	SIN3A	chr10:6182399-6183818	GM12878	blood:	n/a	chr10:6182646-6182659
22	STAT5A	chr10:6182336-6184064	GM12878	blood:	n/a	chr10:6182678-6182686
23	PML	chr10:6182710-6184102	GM12878	blood:	n/a	n/a
24	MTA3	chr10:6182294-6184476	GM12878	blood:	n/a	n/a
25	RCOR1	chr10:6182544-6184106	IMR90	lung:	n/a	n/a
26	JUND	chr10:6182287-6184410	GM12878	blood:	n/a	chr10:6183319-6183331
27	MTA3	chr10:6182771-6184388	GM12878	blood:	n/a	n/a
28	TCF3	chr10:6182401-6182822	GM12878	blood:	n/a	chr10:6182641-6182651
29	ELK1	chr10:6182525-6183765	GM12878	blood:	n/a	chr10:6182624-6182633 chr10:6182624-6182633
30	ZEB1	chr10:6182428-6183159	GM12878	blood:	n/a	n/a
31	BATF	chr10:6182368-6184471	GM12878	blood:	n/a	n/a
32	TBP	chr10:6182510-6184082	GM12878	blood:	n/a	n/a
33	POLR2A	chr10:6182381-6184149	GM12878	blood:	n/a	n/a
34	ZNF263	chr10:6182669-6183838	HEK293-T-REx	kidney:	n/a	chr10:6182678-6182687
35	PBX3	chr10:6182614-6182832	GM12878	blood:	n/a	chr10:6182730-6182739

No.	Distal block	Cell Line	Cell type
1	chr10:6181525..6183322-chr10:6221078..6223708,2	MCF-7	breast:
2	chr10:6060947..6063701-chr10:6181512..6183483,2	K562	blood:
3	chr10:6182309..6185774-chr10:6185942..6188983,5	MCF-7	breast:
4	chr10:6171947..6174676-chr10:6182111..6184339,3	MCF-7	breast:
5	chr10:6180971..6185195-chr10:6203384..6207419,4	MCF-7	breast:

Variant related genes	Relation type
PFKFB3	TF binding region
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11818885	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243993	1.00[ASN][1000 genomes]
rs12250554	1.00[ASN][1000 genomes]
rs12256793	1.00[ASN][1000 genomes]
rs12261272	1.00[ASN][1000 genomes]
rs12722484	1.00[ASN][1000 genomes]
rs12722486	1.00[ASN][1000 genomes]
rs12722505	1.00[ASN][1000 genomes]
rs28360488	1.00[ASN][1000 genomes]
rs28360493	1.00[ASN][1000 genomes]
rs3136615	1.00[ASN][1000 genomes]
rs41294605	1.00[ASN][1000 genomes]
rs41294659	1.00[ASN][1000 genomes]
rs41294663	1.00[ASN][1000 genomes]
rs41294681	1.00[ASN][1000 genomes]
rs41294907	1.00[ASN][1000 genomes]
rs41294937	1.00[ASN][1000 genomes]
rs41295047	1.00[ASN][1000 genomes]
rs41295093	1.00[ASN][1000 genomes]
rs41295115	1.00[ASN][1000 genomes]
rs55998002	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56055806	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56236667	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56249263	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58820784	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60925594	1.00[ASN][1000 genomes]
rs61551084	1.00[ASN][1000 genomes]
rs61839702	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61839723	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839726	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62626315	1.00[ASN][1000 genomes]
rs62626320	1.00[ASN][1000 genomes]
rs62626323	1.00[ASN][1000 genomes]
rs62626344	1.00[ASN][1000 genomes]
rs6602502	1.00[ASN][1000 genomes]
rs72777814	1.00[ASN][1000 genomes]
rs7893324	1.00[ASN][1000 genomes]
rs7898286	1.00[ASN][1000 genomes]
rs8177586	1.00[ASN][1000 genomes]
rs8177587	1.00[ASN][1000 genomes]
rs8177590	1.00[ASN][1000 genomes]
rs8177600	1.00[ASN][1000 genomes]
rs8177613	1.00[ASN][1000 genomes]
rs8177614	1.00[ASN][1000 genomes]
rs8177631	1.00[ASN][1000 genomes]
rs8177633	1.00[ASN][1000 genomes]
rs8177636	1.00[ASN][1000 genomes]
rs8177694	1.00[ASN][1000 genomes]
rs8177755	1.00[ASN][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	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv894816	chr10:6173416-6190343	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv894817	chr10:6173416-6251252	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6171400-6183200	Weak transcription	Right Atrium	heart
2	chr10:6172200-6182800	Weak transcription	Brain Angular Gyrus	brain
3	chr10:6176600-6185000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:6180600-6183400	Weak transcription	Esophagus	oesophagus
5	chr10:6181600-6182800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:6181600-6183200	Enhancers	Fetal Thymus	thymus
7	chr10:6181600-6183600	Enhancers	Spleen	Spleen
8	chr10:6181600-6184000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr10:6181800-6183600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr10:6182000-6182800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
11	chr10:6182000-6182800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr10:6182000-6182800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr10:6182000-6182800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:6182000-6182800	Flanking Active TSS	Dnd41	blood
15	chr10:6182000-6183000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr10:6182000-6183000	Enhancers	Primary hematopoietic stem cells	blood
17	chr10:6182000-6183200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:6182000-6183200	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr10:6182000-6183400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr10:6182000-6183400	Enhancers	Psoas Muscle	Psoas
21	chr10:6182000-6183600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr10:6182000-6183800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr10:6182000-6184000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:6182000-6184400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr10:6182000-6185400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:6182200-6182800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:6182200-6183000	Enhancers	Primary B cells from cord blood	blood
28	chr10:6182200-6183000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:6182200-6183200	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr10:6182200-6183600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr10:6182200-6183600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr10:6182200-6184000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr10:6182200-6184000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr10:6182200-6184000	Flanking Active TSS	GM12878-XiMat	blood
35	chr10:6182400-6182800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
36	chr10:6182400-6182800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr10:6182400-6183000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
38	chr10:6182400-6183000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr10:6182400-6183000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr10:6182400-6183000	Enhancers	HUVEC	blood vessel
41	chr10:6182400-6183000	Enhancers	NH-A	brain
42	chr10:6182400-6183000	Enhancers	NHLF	lung
43	chr10:6182400-6183200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr10:6182400-6183200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr10:6182400-6183200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr10:6182400-6183200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr10:6182400-6183200	Enhancers	Liver	Liver
48	chr10:6182400-6183200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr10:6182400-6183200	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr10:6182400-6183200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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