Variant report

Variant	rs57795346
Chromosome Location	chr3:179042503-179042504
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	MYC	chr3:179041789-179043069	MCF10A-Er-Src	breast:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179042164-179042183
2	BCLAF1	chr3:179042180-179042614	GM12878	blood:	n/a	n/a
3	MYC	chr3:179039897-179042523	MCF10A-Er-Src	breast:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179040898-179040907 chr3:179042164-179042183
4	MYC	chr3:179041962-179042680	NB4	blood:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179042164-179042183
5	IRF1	chr3:179041586-179042635	K562	blood:	n/a	chr3:179042538-179042551 chr3:179041902-179041916 chr3:179042538-179042552 chr3:179041898-179041918 chr3:179041854-179041868 chr3:179041904-179041917 chr3:179041905-179041922 chr3:179042537-179042551 chr3:179041850-179041870 chr3:179041855-179041869 chr3:179041903-179041917 chr3:179042536-179042550 chr3:179041852-179041866 chr3:179041906-179041920
6	MAX	chr3:179040229-179042627	NB4	blood:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179040898-179040907 chr3:179042164-179042183
7	POLR2A	chr3:179042163-179042718	GM12892	blood:	n/a	n/a
8	RAD21	chr3:179039236-179042655	SK-N-SH	brain:	n/a	chr3:179041123-179041133 chr3:179041353-179041367 chr3:179041292-179041302 chr3:179040968-179040980 chr3:179040969-179040982 chr3:179039549-179039568
9	POLR2A	chr3:179039299-179043011	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:179042141-179042606	GM12892	blood:	n/a	n/a
11	UBTF	chr3:179040514-179042581	K562	blood:	n/a	n/a
12	MYC	chr3:179039371-179042652	K562	blood:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179040898-179040907 chr3:179042164-179042183
13	MYC	chr3:179039244-179042670	K562	blood:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179040898-179040907 chr3:179042164-179042183
14	MAX	chr3:179042014-179042562	K562	blood:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179042164-179042183
15	MXI1	chr3:179039283-179042871	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr3:179040497-179042743	K562	blood:	n/a	n/a
17	TEAD4	chr3:179041431-179042515	K562	blood:	n/a	n/a
18	CHD1	chr3:179039333-179042772	IMR90	lung:	n/a	n/a
19	MXI1	chr3:179039982-179042741	IMR90	lung:	n/a	n/a
20	STAT1	chr3:179042330-179042510	GM12878	blood:	n/a	chr3:179042404-179042411
21	MXI1	chr3:179040428-179042705	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:179042205-179043152	GM12878	blood:	n/a	n/a
23	CTCF	chr3:179042480-179042630	HCPEpiC	choroid plexus:	n/a	n/a
24	RFX5	chr3:179039905-179042511	Hela-S3	cervix:	n/a	n/a
25	MXI1	chr3:179041711-179042619	K562	blood:	n/a	n/a
26	MAX	chr3:179040028-179042505	Hela-S3	cervix:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179040898-179040907 chr3:179042164-179042183
27	MYC	chr3:179039379-179042663	K562	blood:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179040898-179040907 chr3:179042164-179042183
28	ZNF263	chr3:179040255-179042852	HEK293-T-REx	kidney:	n/a	chr3:179041089-179041098 chr3:179042473-179042482
29	WRNIP1	chr3:179042251-179042551	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:179042124-179042649	GM12878	blood:	n/a	n/a
31	UBTF	chr3:179040219-179042695	K562	blood:	n/a	n/a
32	BRCA1	chr3:179041190-179042713	Hela-S3	cervix:	n/a	n/a
33	MXI1	chr3:179040230-179042507	Hela-S3	cervix:	n/a	n/a
34	MAX	chr3:179041940-179042507	K562	blood:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179042164-179042183
35	RCOR1	chr3:179042170-179042722	K562	blood:	n/a	n/a
36	TBP	chr3:179042136-179042656	K562	blood:	n/a	n/a
37	IRF1	chr3:179041545-179042720	K562	blood:	n/a	chr3:179042538-179042551 chr3:179041902-179041916 chr3:179042538-179042552 chr3:179041898-179041918 chr3:179041854-179041868 chr3:179041904-179041917 chr3:179041905-179041922 chr3:179042537-179042551 chr3:179041850-179041870 chr3:179041855-179041869 chr3:179041903-179041917 chr3:179042536-179042550 chr3:179041852-179041866 chr3:179041906-179041920
38	POLR2A	chr3:179040110-179042550	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:179039679..179043417-chr3:179063023..179066951,5	K562	blood:
2	chr3:179040252..179043387-chr3:179064355..179067344,4	MCF-7	breast:
3	chr3:179041141..179044648-chr3:179167085..179169566,4	K562	blood:
4	chr3:179040254..179044115-chr3:179063916..179068626,6	K562	blood:
5	chr3:179037868..179043452-chr3:179279283..179282534,12	K562	blood:
6	chr3:179039334..179043117-chr3:179061578..179071936,16	MCF-7	breast:
7	chr3:179040074..179043948-chr3:179167085..179170222,5	K562	blood:
8	chr3:179039352..179043378-chr3:179279283..179282999,10	K562	blood:
9	chr3:179039610..179042933-chr3:179054240..179057497,4	MCF-7	breast:
10	chr3:178866029..178868505-chr3:179041655..179043720,2	K562	blood:
11	chr3:178977854..178979821-chr3:179040251..179043018,2	MCF-7	breast:
12	chr3:179040206..179042939-chr3:179043914..179045418,3	MCF-7	breast:
13	chr3:179040612..179043524-chr3:179043815..179047485,6	K562	blood:
14	chr3:178864492..178868931-chr3:179039553..179043493,6	MCF-7	breast:
15	chr3:179039914..179042763-chr3:179093091..179095772,2	K562	blood:

Variant related genes	Relation type
ZNF639	TF binding region
ENSG00000114450	Chromatin interaction
ENSG00000273190	Chromatin interaction
ENSG00000229102	Chromatin interaction
ENSG00000121864	Chromatin interaction
ENSG00000121879	Chromatin interaction
ENSG00000136518	Chromatin interaction
ENSG00000240429	Chromatin interaction
ENSG00000239255	Chromatin interaction
ENSG00000171109	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11916825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11919840	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11925064	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11925248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927084	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13317510	0.89[AMR][1000 genomes]
rs16830445	0.89[AMR][1000 genomes]
rs16830460	0.89[AMR][1000 genomes]
rs28512433	0.89[AMR][1000 genomes]
rs28522651	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55805052	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56210820	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56265474	0.89[AMR][1000 genomes]
rs56280435	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57148977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57526364	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58741861	0.89[AMR][1000 genomes]
rs59062224	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59333548	0.89[AMR][1000 genomes]
rs59511701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59564372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59833817	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60191176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60746059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61246771	0.89[AMR][1000 genomes]
rs61325843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778235	0.89[AMR][1000 genomes]
rs6800044	0.89[AMR][1000 genomes]
rs6808033	0.89[AMR][1000 genomes]
rs6808866	1.00[AMR][1000 genomes]
rs73043406	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043409	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73043413	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043415	0.97[AFR][1000 genomes]
rs73045191	0.89[AMR][1000 genomes]
rs73045195	0.89[AMR][1000 genomes]
rs73045198	0.89[AMR][1000 genomes]
rs73059758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73059766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355835	0.89[AMR][1000 genomes]
rs73883508	0.89[AMR][1000 genomes]
rs73883509	0.89[AMR][1000 genomes]
rs73886620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7611533	0.89[AMR][1000 genomes]
rs7625719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814990	0.89[AMR][1000 genomes]
rs9829054	0.89[AMR][1000 genomes]
rs9834493	0.89[AMR][1000 genomes]
rs9861354	0.89[AMR][1000 genomes]
rs9864857	0.89[AMR][1000 genomes]
rs9872939	0.89[AMR][1000 genomes]
rs9884070	0.89[AMR][1000 genomes]
rs9968068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription 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 target site	32 gene(s)	inside rSNPs	diseases
9	nsv1010137	chr3:178962897-179050787	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
10	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179038800-179042800	Active TSS	Ovary	ovary
2	chr3:179039000-179043200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:179039200-179042600	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr3:179039200-179042600	Active TSS	Colonic Mucosa	Colon
5	chr3:179039200-179042800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:179039800-179042800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:179040000-179042600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:179040000-179042600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:179040000-179042800	Active TSS	HSMMtube	muscle
10	chr3:179040000-179043000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:179040200-179042600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:179040200-179042800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:179040200-179042800	Active TSS	Aorta	Aorta
14	chr3:179040200-179042800	Active TSS	NHDF-Ad	bronchial
15	chr3:179040400-179042600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:179040400-179042600	Active TSS	Stomach Smooth Muscle	stomach
17	chr3:179040400-179043000	Active TSS	HSMM	muscle
18	chr3:179040400-179043000	Active TSS	Osteobl	bone
19	chr3:179040600-179042800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:179040600-179042800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:179040600-179042800	Active TSS	Fetal Muscle Trunk	muscle
22	chr3:179040600-179043200	Active TSS	GM12878-XiMat	blood
23	chr3:179041000-179042600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:179041200-179042600	Bivalent/Poised TSS	HepG2	liver
25	chr3:179041400-179042600	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr3:179041400-179042600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr3:179041600-179042600	Flanking Active TSS	Liver	Liver
28	chr3:179041600-179042600	Active TSS	Brain Germinal Matrix	brain
29	chr3:179041600-179042600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr3:179041600-179042800	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr3:179041600-179042800	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr3:179041600-179042800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:179041600-179042800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:179041600-179042800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:179041600-179042800	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr3:179041600-179042800	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr3:179041600-179043000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:179041800-179042600	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr3:179041800-179042800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:179041800-179042800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr3:179041800-179042800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:179041800-179042800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr3:179041800-179042800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr3:179041800-179043000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:179041800-179043000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr3:179041800-179046600	Weak transcription	Gastric	stomach
47	chr3:179041800-179046600	Weak transcription	Small Intestine	intestine
48	chr3:179041800-179048000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:179042000-179042600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr3:179042000-179042600	Flanking Active TSS	Brain Cingulate Gyrus	brain

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