Variant report

Variant	rs4569075
Chromosome Location	chr12:50066801-50066802
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	BHLHE40	chr12:50066442-50066899	GM12878	blood:	n/a	n/a
2	RELA	chr12:50066307-50066935	GM12892	blood:	n/a	n/a
3	CTCF	chr12:50066740-50066890	HAc	cerebellar:	n/a	chr12:50066789-50066798
4	RELA	chr12:50066301-50066934	GM10847	blood:	n/a	n/a
5	CTCF	chr12:50066660-50066810	HCFaa	heart:	n/a	chr12:50066789-50066798
6	RELA	chr12:50064647-50067064	GM12891	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255
7	MTA3	chr12:50066319-50066879	GM12878	blood:	n/a	n/a
8	RUNX3	chr12:50066250-50067254	GM12878	blood:	n/a	n/a
9	FOXM1	chr12:50066107-50067143	GM12878	blood:	n/a	n/a
10	RELA	chr12:50066189-50066897	GM15510	blood:	n/a	n/a
11	RELA	chr12:50064419-50067389	GM19193	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255
12	EBF1	chr12:50066779-50067121	GM12878	blood:	n/a	n/a
13	RELA	chr12:50066122-50067433	GM18951	blood:	n/a	n/a
14	MXI1	chr12:50066670-50068551	IMR90	lung:	n/a	n/a
15	ZNF143	chr12:50066465-50067002	GM12878	blood:	n/a	n/a
16	CTCF	chr12:50066660-50066810	HBMEC	blood vessel:	n/a	chr12:50066789-50066798
17	CTCF	chr12:50066700-50066850	Caco-2	colon:	n/a	chr12:50066789-50066798
18	MTA3	chr12:50065848-50067551	GM12878	blood:	n/a	n/a
19	EBF1	chr12:50066369-50067271	GM12878	blood:	n/a	n/a
20	NFATC1	chr12:50066176-50066843	GM12878	blood:	n/a	n/a
21	RELA	chr12:50064591-50067007	GM19099	blood:	n/a	chr12:50065248-50065257 chr12:50065246-50065255 chr12:50065248-50065257 chr12:50065246-50065255
22	STAT3	chr12:50066703-50066813	MCF10A-Er-Src	breast:	n/a	chr12:50066727-50066739
23	CTCF	chr12:50066680-50066830	AoAF	blood vessel:	n/a	chr12:50066789-50066798
24	RELA	chr12:50066142-50067148	GM18505	blood:	n/a	n/a
25	EBF1	chr12:50066758-50067136	GM12878	blood:	n/a	n/a
26	NFIC	chr12:50065810-50066903	GM12878	blood:	n/a	n/a
27	CTCF	chr12:50066720-50066870	HCPEpiC	choroid plexus:	n/a	chr12:50066789-50066798
28	CTCF	chr12:50066720-50066870	AoAF	blood vessel:	n/a	chr12:50066789-50066798
29	CTCF	chr12:50066760-50066910	HPAF	blood vessel:	n/a	chr12:50066789-50066798
30	RUNX3	chr12:50066240-50067351	GM12878	blood:	n/a	n/a
31	RELA	chr12:50066105-50067173	GM12878	blood:	n/a	n/a
32	FOXA2	chr12:50066697-50066924	HepG2	liver:	n/a	chr12:50066797-50066809
33	IKZF1	chr12:50065978-50066931	GM12878	blood:	n/a	n/a
34	CTCF	chr12:50066720-50066870	HPAF	blood vessel:	n/a	chr12:50066789-50066798
35	CTCF	chr12:50066780-50066930	HBMEC	blood vessel:	n/a	chr12:50066789-50066798

No.	Distal block	Cell Line	Cell type
1	chr12:50065718..50069326-chr12:50125302..50127957,3	K562	blood:
2	chr12:50050102..50052807-chr12:50065417..50067825,2	K562	blood:
3	chr12:50062633..50068951-chr12:50134385..50140154,8	K562	blood:
4	chr12:50059879..50062225-chr12:50063774..50067547,4	K562	blood:
5	chr12:50064210..50067102-chr12:50135101..50137236,3	K562	blood:
6	chr12:50054963..50057045-chr12:50065991..50068572,3	K562	blood:
7	chr12:50016535..50018168-chr12:50064664..50066809,2	K562	blood:
8	chr12:50066175..50068343-chr12:50098186..50100084,3	K562	blood:
9	chr12:50058474..50062820-chr12:50063991..50067805,5	MCF-7	breast:
10	chr12:50066009..50068301-chr12:50069038..50071401,2	K562	blood:
11	chr12:50066343..50069112-chr12:50133509..50136690,4	MCF-7	breast:
12	chr12:50065969..50068241-chr12:50076218..50078635,2	K562	blood:
13	chr12:50048532..50051602-chr12:50065327..50069233,3	K562	blood:

Variant related genes	Relation type
FMNL3	TF binding region
ENSG00000161791	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11169048	1.00[CHB][hapmap]
rs11169058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12296440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12305716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12309053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12315996	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12322561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123865	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17123919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs17123922	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs17123943	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs17197593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4144469	1.00[JPT][hapmap]
rs7294648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7294973	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7976165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9919740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50042400-50067000	Weak transcription	Fetal Brain Male	brain
2	chr12:50052600-50067000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:50052600-50067400	Weak transcription	Fetal Brain Female	brain
4	chr12:50054400-50069800	Enhancers	Left Ventricle	heart
5	chr12:50057600-50067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:50057600-50067000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:50057600-50067200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:50058400-50067200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:50060400-50069400	Enhancers	Fetal Thymus	thymus
10	chr12:50062000-50069600	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:50062200-50067000	Enhancers	Brain Anterior Caudate	brain
12	chr12:50063200-50069200	Enhancers	Thymus	Thymus
13	chr12:50063200-50069400	Enhancers	Lung	lung
14	chr12:50063200-50069800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:50063400-50068200	Enhancers	Spleen	Spleen
16	chr12:50063600-50069200	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:50063600-50069400	Enhancers	Right Atrium	heart
18	chr12:50063800-50069400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:50063800-50069400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr12:50063800-50069400	Enhancers	Right Ventricle	heart
21	chr12:50063800-50070000	Enhancers	Psoas Muscle	Psoas
22	chr12:50063800-50070200	Enhancers	Ovary	ovary
23	chr12:50063800-50070600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:50063800-50070600	Enhancers	Fetal Lung	lung
25	chr12:50064000-50067200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr12:50064200-50068000	Enhancers	Liver	Liver
27	chr12:50064200-50068400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:50064200-50068600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:50064200-50070000	Enhancers	Fetal Muscle Leg	muscle
30	chr12:50064400-50067000	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr12:50064400-50067400	Enhancers	Gastric	stomach
32	chr12:50064400-50067600	Enhancers	HSMMtube	muscle
33	chr12:50064400-50069400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:50064400-50069400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:50064400-50069400	Enhancers	Stomach Mucosa	stomach
36	chr12:50064400-50069600	Enhancers	Placenta	Placenta
37	chr12:50064600-50067000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:50064600-50067000	Enhancers	K562	blood
39	chr12:50064600-50069000	Enhancers	NH-A	brain
40	chr12:50064600-50069400	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr12:50064600-50069600	Enhancers	Small Intestine	intestine
42	chr12:50064600-50070200	Enhancers	Fetal Heart	heart
43	chr12:50064600-50070200	Enhancers	Fetal Stomach	stomach
44	chr12:50064800-50067200	Enhancers	Fetal Kidney	kidney
45	chr12:50064800-50067600	Enhancers	NHDF-Ad	bronchial
46	chr12:50065000-50067600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:50065000-50067600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:50065000-50069000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:50065000-50069400	Enhancers	Fetal Intestine Large	intestine
50	chr12:50065200-50067800	Enhancers	Primary B cells from cord blood	blood

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