Variant report

Variant	rs10056202
Chromosome Location	chr5:60459405-60459406
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	FOXA2	chr5:60458793-60459462	HepG2	liver:	n/a	chr5:60458984-60458996
2	CEBPB	chr5:60458741-60459421	HepG2	liver:	n/a	n/a
3	MTA3	chr5:60457455-60459572	GM12878	blood:	n/a	n/a
4	FOS	chr5:60459136-60459516	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:60457621-60459424	GM12878	blood:	n/a	n/a
6	MTA3	chr5:60457732-60459453	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:60457838-60459414	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:60458904-60459572	PANC-1	pancreas:	n/a	n/a
9	ARID3A	chr5:60457952-60459426	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:60457563-60460493	GM12891	blood:	n/a	n/a
11	POLR2A	chr5:60457246-60460035	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:60457646-60459592	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:60455764-60460434	K562	blood:	n/a	n/a
14	STAT3	chr5:60459095-60459445	MCF10A-Er-Src	breast:	n/a	n/a
15	ATF2	chr5:60457869-60459425	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:60457661-60459418	K562	blood:	n/a	n/a
17	JUND	chr5:60457762-60459427	K562	blood:	n/a	chr5:60458486-60458495
18	POLR2A	chr5:60457553-60459409	GM12892	blood:	n/a	n/a
19	HCFC1	chr5:60457220-60459753	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:60457331-60460406	GM12878	blood:	n/a	n/a
21	TBL1XR1	chr5:60457986-60459560	K562	blood:	n/a	n/a
22	FOXA1	chr5:60458857-60459410	HepG2	liver:	n/a	chr5:60459132-60459147 chr5:60458984-60458996
23	POLR2A	chr5:60457726-60459721	IMR90	lung:	n/a	n/a
24	POLR2A	chr5:60457247-60459892	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr5:60457682-60459432	GM12892	blood:	n/a	n/a
26	FOXA1	chr5:60458871-60459466	T-47D	breast:	n/a	chr5:60459132-60459147 chr5:60458984-60458996
27	POLR2A	chr5:60457156-60460506	MCF10A-Er-Src	breast:	n/a	n/a
28	FOXA1	chr5:60458879-60459406	HepG2	liver:	n/a	chr5:60459132-60459147 chr5:60458984-60458996
29	KAP1	chr5:60459067-60459513	U2OS	brain:	n/a	n/a
30	FOXA1	chr5:60458738-60459512	T-47D	breast:	n/a	chr5:60459132-60459147 chr5:60458984-60458996
31	MXI1	chr5:60457331-60460236	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr5:60457596-60460211	SK-N-MC	brain:	n/a	n/a
33	GATA3	chr5:60459324-60459501	SH-SY5Y	brain:	n/a	n/a
34	CHD1	chr5:60457169-60459652	IMR90	lung:	n/a	n/a
35	RUNX3	chr5:60457675-60459473	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:60457602-60459452	HepG2	liver:	n/a	n/a
37	PML	chr5:60457533-60459502	GM12878	blood:	n/a	n/a
38	POLR2A	chr5:60457713-60459454	MCF-7	breast:	n/a	n/a
39	POLR2A	chr5:60459214-60459446	ProgFib	skin:	n/a	n/a
40	NFIC	chr5:60457640-60459498	GM12878	blood:	n/a	n/a
41	CEBPB	chr5:60459093-60459447	IMR90	lung:	n/a	n/a
42	POLR2A	chr5:60457578-60460024	GM19099	blood:	n/a	n/a
43	FOS	chr5:60459097-60459436	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr5:60457562-60459692	GM18505	blood:	n/a	n/a
45	GATA3	chr5:60458925-60459613	MCF-7	breast:	n/a	n/a
46	ARID3A	chr5:60459138-60459436	K562	blood:	n/a	n/a
47	POLR2A	chr5:60459352-60459599	Hela-S3	cervix:	n/a	n/a
48	MAX	chr5:60457608-60459483	HepG2	liver:	n/a	chr5:60458426-60458436 chr5:60458430-60458440
49	POLR2A	chr5:60457642-60460052	MCF10A-Er-Src	breast:	n/a	n/a
50	CEBPB	chr5:60459075-60459428	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:60456297..60461829-chr5:60626718..60632720,8	K562	blood:
2	chr17:57967665..57970523-chr5:60456925..60459540,2	MCF-7	breast:
3	chr5:60428916..60430499-chr5:60459028..60461996,2	K562	blood:
4	chr5:60454421..60471345-chr5:60622342..60633215,36	MCF-7	breast:
5	chr5:60454193..60465680-chr5:60622262..60629761,38	MCF-7	breast:
6	chr5:60456802..60459800-chr5:60641121..60644130,3	MCF-7	breast:
7	chr5:59994474..59997876-chr5:60455928..60460228,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDUFAF2-2	chr5:60458334-60460554	NONHSAT101658

Variant related genes	Relation type
SMIM15	TF binding region
ENSG00000035499	Chromatin interaction
ENSG00000251682	Chromatin interaction
ENSG00000108443	Chromatin interaction
ENSG00000108423	Chromatin interaction
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10035893	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10043790	0.87[AMR][1000 genomes]
rs10044183	1.00[AMR][1000 genomes]
rs10050696	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10051150	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs10056513	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10058726	1.00[AMR][1000 genomes]
rs10064129	1.00[AMR][1000 genomes]
rs10064292	0.87[AMR][1000 genomes]
rs10067476	0.87[AMR][1000 genomes]
rs10069623	1.00[AMR][1000 genomes]
rs10077508	1.00[AMR][1000 genomes]
rs10471504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12110162	1.00[AMR][1000 genomes]
rs12696977	0.87[AMR][1000 genomes]
rs13353957	1.00[AMR][1000 genomes]
rs13355940	0.87[AMR][1000 genomes]
rs13360962	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13362092	0.87[AMR][1000 genomes]
rs2045678	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2161199	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28411035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28446443	1.00[AMR][1000 genomes]
rs28534860	1.00[AMR][1000 genomes]
rs28582880	1.00[AMR][1000 genomes]
rs28781684	0.87[AMR][1000 genomes]
rs28816681	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28882716	1.00[AMR][1000 genomes]
rs28888995	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4647029	0.87[AMR][1000 genomes]
rs4647036	0.87[AMR][1000 genomes]
rs4647061	0.87[AMR][1000 genomes]
rs4647079	1.00[AMR][1000 genomes]
rs4647086	0.87[AMR][1000 genomes]
rs56791802	0.87[AMR][1000 genomes]
rs57818831	0.87[AMR][1000 genomes]
rs58495922	0.87[AMR][1000 genomes]
rs59030859	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6887938	1.00[AMR][1000 genomes]
rs6894736	1.00[AMR][1000 genomes]
rs73095990	0.87[AMR][1000 genomes]
rs73095991	1.00[AMR][1000 genomes]
rs73095993	0.87[AMR][1000 genomes]
rs73099808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099809	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099811	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73114340	1.00[AMR][1000 genomes]
rs7704436	0.87[AMR][1000 genomes]
rs7716539	1.00[AMR][1000 genomes]
rs7720240	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7728655	0.87[AMR][1000 genomes]
rs7731888	1.00[AMR][1000 genomes]
rs7734656	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7735610	0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9291698	1.00[AMR][1000 genomes]
rs9291699	0.87[AMR][1000 genomes]
rs9291703	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9968618	0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60456600-60459600	Active TSS	Psoas Muscle	Psoas
2	chr5:60456800-60459600	Active TSS	HSMMtube	muscle
3	chr5:60456800-60459800	Active TSS	NHDF-Ad	bronchial
4	chr5:60457000-60459600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:60457000-60459600	Active TSS	Fetal Kidney	kidney
6	chr5:60457000-60459800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:60457000-60459800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:60457000-60460000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:60457000-60460000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:60457000-60460200	Active TSS	A549	lung
11	chr5:60457200-60459600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:60457200-60459600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:60457200-60459800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr5:60457200-60459800	Active TSS	H1 Cell Line	embryonic stem cell
15	chr5:60457200-60459800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:60457200-60459800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:60457200-60459800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:60457200-60459800	Active TSS	Fetal Muscle Trunk	muscle
19	chr5:60457200-60459800	Active TSS	Stomach Smooth Muscle	stomach
20	chr5:60457400-60459600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr5:60457400-60459600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:60457400-60459600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr5:60458600-60459600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr5:60458600-60459600	Flanking Active TSS	NH-A	brain
25	chr5:60458600-60459800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:60458800-60459600	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr5:60458800-60459600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr5:60458800-60459600	Flanking Active TSS	Hela-S3	cervix
29	chr5:60458800-60459800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:60458800-60459800	Flanking Active TSS	Fetal Brain Female	brain
31	chr5:60459000-60459600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:60459000-60459600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:60459000-60459600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr5:60459000-60459600	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr5:60459000-60459600	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr5:60459000-60459600	Weak transcription	Placenta	Placenta
37	chr5:60459000-60459600	Weak transcription	Gastric	stomach
38	chr5:60459000-60459800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:60459000-60459800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:60459000-60459800	Weak transcription	Lung	lung
41	chr5:60459000-60459800	Flanking Active TSS	Osteobl	bone
42	chr5:60459000-60460000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:60459000-60460000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr5:60459000-60460000	Flanking Active TSS	Fetal Heart	heart
45	chr5:60459000-60460200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr5:60459000-60460200	Enhancers	Spleen	Spleen
47	chr5:60459200-60459600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:60459200-60459600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:60459200-60459600	Weak transcription	Esophagus	oesophagus
50	chr5:60459200-60459600	Flanking Active TSS	Fetal Brain Male	brain

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