Variant report

Variant	rs10059245
Chromosome Location	chr5:95170870-95170871
allele	C/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	MAX	chr5:95170285-95171065	A549	lung:	n/a	n/a
2	CTCF	chr5:95170740-95170890	HPAF	blood vessel:	n/a	chr5:95170850-95170863
3	YY1	chr5:95170509-95170917	H1-hESC	embryonic stem cell:	n/a	chr5:95170848-95170857
4	CTCF	chr5:95170760-95170910	GM12872	blood:	n/a	chr5:95170850-95170863
5	ATF2	chr5:95170026-95170881	GM12878	blood:	n/a	n/a
6	REST	chr5:95170481-95170997	A549	lung:	n/a	n/a
7	PAX5	chr5:95170546-95170879	GM12892	blood:	n/a	n/a
8	POLR2A	chr5:95170360-95170973	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr5:95170630-95170953	T-47D	breast:	n/a	chr5:95170850-95170863
10	CTCF	chr5:95170617-95170953	IMR90	lung:	n/a	chr5:95170850-95170863
11	POLR2A	chr5:95170363-95170919	Hela-S3	cervix:	n/a	n/a
12	PML	chr5:95170013-95171046	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:95170364-95170871	HepG2	liver:	n/a	n/a
14	POLR2A	chr5:95170214-95170956	HepG2	liver:	n/a	n/a
15	CTCF	chr5:95170696-95170917	A549	lung:	n/a	chr5:95170850-95170863
16	CTCF	chr5:95170740-95170890	GM12867	blood:	n/a	chr5:95170850-95170863
17	CEBPB	chr5:95170241-95170919	H1-hESC	embryonic stem cell:	n/a	chr5:95170445-95170456
18	CTCF	chr5:95170740-95170890	GM12866	blood:	n/a	chr5:95170850-95170863
19	JUND	chr5:95170706-95170884	HepG2	liver:	n/a	n/a
20	POLR2A	chr5:95170292-95170959	MCF-7	breast:	n/a	n/a
21	POU2F2	chr5:95170123-95170966	GM12878	blood:	n/a	n/a
22	CTCF	chr5:95170740-95170890	GM12872	blood:	n/a	chr5:95170850-95170863
23	YY1	chr5:95170644-95170872	A549	lung:	n/a	chr5:95170848-95170857
24	CTCF	chr5:95170686-95170912	GM12878	blood:	n/a	chr5:95170850-95170863
25	MAX	chr5:95170592-95170939	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:95170220-95171055	GM19099	blood:	n/a	n/a
27	ZNF143	chr5:95170643-95170917	H1-hESC	embryonic stem cell:	n/a	n/a
28	BCLAF1	chr5:95170454-95170940	GM12878	blood:	n/a	chr5:95170809-95170822
29	MYBL2	chr5:95170425-95171043	HepG2	liver:	n/a	n/a
30	POLR2A	chr5:95170584-95170898	GM12891	blood:	n/a	n/a
31	YY1	chr5:95170445-95170914	GM12878	blood:	n/a	chr5:95170848-95170857
32	RAD21	chr5:95170608-95171013	A549	lung:	n/a	n/a
33	CTCF	chr5:95170740-95170890	GM12864	blood:	n/a	chr5:95170850-95170863
34	E2F6	chr5:95170573-95170932	A549	lung:	n/a	n/a
35	RUNX3	chr5:95170463-95171021	GM12878	blood:	n/a	n/a
36	BCLAF1	chr5:95170509-95171071	GM12878	blood:	n/a	chr5:95170809-95170822
37	ELF1	chr5:95170239-95170964	GM12878	blood:	n/a	chr5:95170848-95170857
38	POLR2A	chr5:95169767-95172654	GM12891	blood:	n/a	n/a
39	ZKSCAN1	chr5:95170615-95170926	Hela-S3	cervix:	n/a	n/a
40	MAX	chr5:95170449-95171023	HepG2	liver:	n/a	n/a
41	YY1	chr5:95170515-95170970	SK-N-SH	brain:	n/a	chr5:95170848-95170857
42	CTCF	chr5:95170664-95170898	H1-hESC	embryonic stem cell:	n/a	chr5:95170850-95170863
43	RAD21	chr5:95170596-95170978	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr5:95170606-95170939	GM19238	blood:	n/a	chr5:95170850-95170863
45	POLR2A	chr5:95170468-95170929	HL-60	blood:	n/a	n/a
46	ZNF143	chr5:95170668-95170942	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr5:95170359-95171025	NB4	blood:	n/a	n/a
48	CTCF	chr5:95170701-95170881	HepG2	liver:	n/a	chr5:95170850-95170863
49	GTF2F1	chr5:95170663-95170967	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr5:95170401-95170962	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:94981172..94985318-chr5:95169805..95176246,5	MCF-7	breast:
2	chr5:95157133..95161008-chr5:95170364..95173601,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251000	TF binding region
ENSG00000175449	Chromatin interaction
ENSG00000173221	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10040697	0.81[CEU][hapmap]
rs10059130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067881	1.00[ASN][1000 genomes]
rs10074815	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10515230	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57148774	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6556884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6556885	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6556886	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6556891	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67807434	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68044534	0.94[ASN][1000 genomes]
rs68095140	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785409	1.00[ASN][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	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv882389	chr5:95144952-95173887	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10059245	AC008592.3	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95161600-95171400	Weak transcription	Small Intestine	intestine
2	chr5:95164200-95171400	Weak transcription	Spleen	Spleen
3	chr5:95169800-95171200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:95169800-95171400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:95169800-95171400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr5:95169800-95171400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:95169800-95171400	Active TSS	Right Ventricle	heart
8	chr5:95169800-95171600	Active TSS	Rectal Smooth Muscle	rectum
9	chr5:95169800-95171600	Active TSS	Stomach Smooth Muscle	stomach
10	chr5:95169800-95171800	Active TSS	Brain Cingulate Gyrus	brain
11	chr5:95170000-95171000	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr5:95170000-95171000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr5:95170000-95171000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:95170000-95171000	Active TSS	Fetal Kidney	kidney
15	chr5:95170000-95171200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr5:95170000-95171200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:95170000-95171200	Active TSS	Brain Anterior Caudate	brain
18	chr5:95170000-95171200	Active TSS	Brain Hippocampus Middle	brain
19	chr5:95170000-95171200	Active TSS	Duodenum Mucosa	Duodenum
20	chr5:95170000-95171200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr5:95170000-95171200	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr5:95170000-95171200	Active TSS	A549	lung
23	chr5:95170000-95171200	Active TSS	Hela-S3	cervix
24	chr5:95170000-95171400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr5:95170000-95171400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:95170000-95171400	Active TSS	Right Atrium	heart
27	chr5:95170000-95171400	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr5:95170000-95171400	Active TSS	GM12878-XiMat	blood
29	chr5:95170000-95172200	Active TSS	Psoas Muscle	Psoas
30	chr5:95170200-95171000	Active TSS	H1 Cell Line	embryonic stem cell
31	chr5:95170200-95171000	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr5:95170200-95171000	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr5:95170200-95171000	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr5:95170200-95171000	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr5:95170200-95171000	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr5:95170200-95171000	Active TSS	Adipose Nuclei	Adipose
37	chr5:95170200-95171000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr5:95170200-95171000	Active TSS	Fetal Brain Female	brain
39	chr5:95170200-95171000	Active TSS	Fetal Lung	lung
40	chr5:95170200-95171000	Active TSS	Fetal Muscle Leg	muscle
41	chr5:95170200-95171000	Active TSS	Fetal Stomach	stomach
42	chr5:95170200-95171000	Active TSS	Ovary	ovary
43	chr5:95170200-95171000	Active TSS	NHEK	skin
44	chr5:95170200-95171200	Active TSS	Primary B cells from peripheral blood	blood
45	chr5:95170200-95171200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr5:95170200-95171200	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr5:95170200-95171200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:95170200-95171200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr5:95170200-95171200	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr5:95170200-95171200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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