Variant report

Variant	rs56369297
Chromosome Location	chr10:5946643-5946644
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	CREB1	chr10:5946028-5946797	GM12878	blood:	n/a	n/a
2	NFIC	chr10:5946024-5946946	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:5946181-5946662	GM12878	blood:	n/a	n/a
4	ATF2	chr10:5946041-5946728	GM12878	blood:	n/a	n/a
5	TCF3	chr10:5946001-5946645	GM12878	blood:	n/a	n/a
6	EBF1	chr10:5946036-5946648	GM12878	blood:	n/a	n/a
7	BCLAF1	chr10:5945944-5946697	GM12878	blood:	n/a	n/a
8	RUNX3	chr10:5946165-5946670	GM12878	blood:	n/a	n/a
9	ZNF384	chr10:5946373-5946865	GM12878	blood:	n/a	n/a
10	NFATC1	chr10:5946071-5946670	GM12878	blood:	n/a	chr10:5946320-5946334
11	BCLAF1	chr10:5946112-5946719	GM12878	blood:	n/a	n/a
12	RUNX3	chr10:5946050-5946649	GM12878	blood:	n/a	n/a
13	POLR2A	chr10:5945987-5946685	GM12878	blood:	n/a	n/a
14	FOXM1	chr10:5945906-5946747	GM12878	blood:	n/a	n/a
15	MEF2A	chr10:5946130-5946679	GM12878	blood:	n/a	n/a
16	MTA3	chr10:5945943-5946755	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr10:5946195-5946677	GM12878	blood:	n/a	n/a
18	MEF2C	chr10:5946035-5946697	GM12878	blood:	n/a	chr10:5946397-5946412
19	PML	chr10:5945819-5946821	GM12878	blood:	n/a	n/a
20	IKZF1	chr10:5945733-5946914	GM12878	blood:	n/a	n/a
21	CREB1	chr10:5946025-5946668	GM12878	blood:	n/a	n/a
22	NFIC	chr10:5945957-5947016	GM12878	blood:	n/a	n/a
23	MEF2A	chr10:5946035-5946906	GM12878	blood:	n/a	n/a
24	FOXM1	chr10:5946068-5946711	GM12878	blood:	n/a	n/a
25	NFATC1	chr10:5946059-5946673	GM12878	blood:	n/a	chr10:5946320-5946334
26	ATF2	chr10:5946150-5946660	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:5940356..5945616-chr10:5946052..5950228,5	K562	blood:
2	chr10:5930850..5933132-chr10:5945208..5947286,2	MCF-7	breast:
3	chr10:5934107..5937505-chr10:5944279..5947723,3	K562	blood:
4	chr10:5944902..5949074-chr10:5954801..5958061,6	K562	blood:

Variant related genes	Relation type
FBXO18	TF binding region
ENSG00000134452	Chromatin interaction
ENSG00000134461	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10508298	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508299	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255698	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255774	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255780	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255971	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255974	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256009	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360409	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12767690	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774228	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774886	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12781700	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785055	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17319759	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976655	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985072	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387092	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049919	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61832959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6602330	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090411	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893735	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919913	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[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	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS 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	17 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	chr10:5933200-5948200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:5933200-5949800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:5933200-5977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:5933400-5948200	Weak transcription	Ovary	ovary
5	chr10:5933400-5948400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:5933400-5949800	Weak transcription	Fetal Brain Male	brain
7	chr10:5933600-5948200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr10:5933600-5951600	Weak transcription	Stomach Mucosa	stomach
9	chr10:5934800-5948000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:5935200-5947400	Weak transcription	Small Intestine	intestine
11	chr10:5935600-5962000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr10:5936600-5952600	Weak transcription	Hela-S3	cervix
13	chr10:5936800-5953200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr10:5937200-5947600	Weak transcription	Psoas Muscle	Psoas
15	chr10:5937200-5948000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:5937200-5948000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:5937200-5948400	Weak transcription	Fetal Kidney	kidney
18	chr10:5937400-5948200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr10:5937800-5947600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:5937800-5947600	Weak transcription	HSMM	muscle
21	chr10:5937800-5948000	Weak transcription	Brain Angular Gyrus	brain
22	chr10:5937800-5948200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr10:5938000-5947600	Weak transcription	HSMMtube	muscle
24	chr10:5938000-5947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr10:5938000-5948000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr10:5938000-5948200	Weak transcription	HMEC	breast
27	chr10:5938000-5950800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr10:5938200-5947200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr10:5938200-5947600	Weak transcription	Brain Anterior Caudate	brain
30	chr10:5938200-5947800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:5938200-5948000	Weak transcription	Aorta	Aorta
32	chr10:5938200-5950800	Weak transcription	NH-A	brain
33	chr10:5938400-5947000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:5938400-5947600	Weak transcription	HepG2	liver
35	chr10:5938400-5947800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr10:5938400-5948000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr10:5938600-5947200	Weak transcription	Fetal Intestine Large	intestine
38	chr10:5938600-5947600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr10:5938600-5947800	Weak transcription	HUVEC	blood vessel
40	chr10:5938600-5948000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr10:5938600-5948200	Weak transcription	Brain Substantia Nigra	brain
42	chr10:5938800-5947800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr10:5938800-5948000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr10:5939000-5947600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:5939000-5947600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr10:5939200-5947600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:5939200-5947600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr10:5939400-5947600	Weak transcription	Brain Germinal Matrix	brain
49	chr10:5939400-5948000	Weak transcription	Primary B cells from cord blood	blood
50	chr10:5939400-5948000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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