Variant report

Variant	rs1258188
Chromosome Location	chr10:50976378-50976379
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr10:50976254-50976518	GM12892	blood:	n/a	chr10:50976368-50976386 chr10:50976366-50976385
2	MAX	chr10:50976243-50977281	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr10:50975807-50977321	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr10:50975812-50976504	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr10:50976188-50977299	H1-hESC	embryonic stem cell:	n/a	chr10:50977129-50977138 chr10:50976810-50976819
6	E2F6	chr10:50975840-50977410	H1-hESC	embryonic stem cell:	n/a	chr10:50977129-50977138 chr10:50976810-50976819

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:50976348-50976398	SK-N-MC	brain:	n/a
2	chr10:50976348-50976398	NH-A	brain:	n/a
3	chr10:50976348-50976398	HNPCEpiC	eye:	n/a
4	chr10:50976348-50976398	HCM	heart:	n/a
5	chr10:50976348-50976398	HRPEpiC	eye:	n/a
6	chr10:50976348-50976398	PrEC	prostate:	n/a
7	chr10:50976348-50976398	HepG2	liver:	n/a
8	chr10:50976348-50976398	NB4	blood:	n/a
9	chr10:50976348-50976398	NHDF-neo	bronchial:	n/a
10	chr10:50976348-50976398	A549	lung:	n/a
11	chr10:50976348-50976398	BJ	skin:	n/a
12	chr10:50976348-50976398	AG09309	skin:	n/a
13	chr10:50976348-50976398	SK-N-SH	brain:	n/a
14	chr10:50976348-50976398	ProgFib	skin:	n/a
15	chr10:50976348-50976398	HRE	kidney:	n/a
16	chr10:50976348-50976398	Hepatocyte	liver:	n/a
17	chr10:50976348-50976398	MCF-7	breast:	n/a
18	chr10:50976348-50976398	IMR90	lung:	fetal
19	chr10:50976348-50976398	Hela-S3	cervix:	n/a
20	chr10:50976348-50976398	CMK	blood:	n/a
21	chr10:50976348-50976398	Caco-2	colon:	n/a
22	chr10:50976348-50976398	GM06990	blood:	n/a
23	chr10:50976348-50976398	NHBE	bronchial:	n/a
24	chr10:50976348-50976398	RPTEC	kidney:	n/a
25	chr10:50976348-50976398	T-47D	breast:	n/a
26	chr10:50976348-50976398	HIPEpiC	eye:	n/a
27	chr10:50976348-50976398	HUVEC	blood vessel:	n/a
28	chr10:50976348-50976398	HPAEpiC	pulmonary alveolar:	n/a
29	chr10:50976348-50976398	H1-hESC	embryonic stem cell:	embryo
30	chr10:50976348-50976398	HMEC	breast:	n/a
31	chr10:50976348-50976398	Jurkat	blood:	n/a
32	chr10:50976348-50976398	U87	brain:	n/a
33	chr10:50976348-50976398	HCPEpiC	choroid plexus:	n/a
34	chr10:50976348-50976398	NT2-D1	testis:	n/a
35	chr10:50976348-50976398	SAEC	small airway:	n/a
36	chr10:50976348-50976398	BE2_C	brain:	n/a
37	chr10:50976348-50976398	HEEpiC	esophagus:	n/a
38	chr10:50976348-50976398	HEK293	kidney:	embryo
39	chr10:50976348-50976398	GM12878	blood:	n/a
40	chr10:50976348-50976398	HL-60	blood:	n/a
41	chr10:50976348-50976398	HRCEpiC	kidney:	n/a
42	chr10:50976348-50976398	GM19239	blood:	n/a
43	chr10:50976348-50976398	HCT-116	colon:	n/a
44	chr10:50976348-50976398	MCF10A-Er-Src	breast:	n/a
45	chr10:50976348-50976398	SKMC	muscle:	n/a
46	chr10:50976348-50976398	SK-N-SH_RA	brain:	n/a
47	chr10:50976348-50976398	AG04450	lung:	fetal
48	chr10:50976348-50976398	AoSMC	blood vessel:	n/a
49	chr10:50976348-50976398	ECC-1	luminal epithelium:	n/a
50	chr10:50976348-50976398	GM12892	blood:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50967343..50969554-chr10:50974712..50977623,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226389	TF binding region
ENSG00000226389	CpG island

Extended variants
information (count: 10 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1258186	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1258198	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs717721	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1048905	chr10:50928727-51019190	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv2758219	chr10:50971974-51925166	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv2759749	chr10:50971974-51925166	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv428232	chr10:50971974-51925166	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1258188	AGAP6	cis	Artery Tibial	GTEx
rs1258188	AGAP6	cis	Esophagus Mucosa	GTEx
rs1258188	AGAP6	cis	Adipose Subcutaneous	GTEx
rs1258188	AGAP6	cis	Thyroid	GTEx
rs1258188	AGAP6	cis	Whole Blood	GTEx
rs1258188	AGAP6	cis	Nerve Tibial	GTEx
rs1258188	AGAP6	cis	Esophagus Muscularis	GTEx
rs1258188	AGAP6	cis	lung	GTEx
rs1258188	AGAP6	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50976000-50976400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
2	chr10:50976000-50976600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:50976000-50977200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr10:50976200-50976400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
5	chr10:50976200-50976400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:50976200-50976400	Bivalent Enhancer	Brain Germinal Matrix	brain
7	chr10:50976200-50976600	Bivalent Enhancer	Fetal Brain Male	brain
8	chr10:50976200-50976600	ZNF genes & repeats	Spleen	Spleen
9	chr10:50976200-50977200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
10	chr10:50976200-50977400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin

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