Variant report

Variant	rs1258175
Chromosome Location	chr10:50956905-50956906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50950802..50953710-chr10:50955807..50957980,3	K562	blood:
2	chr10:50953927..50957241-chr10:50965194..50969750,5	K562	blood:
3	chr10:50954773..50957241-chr10:50965884..50969750,3	K562	blood:

Variant related genes	Relation type
ENSG00000197444	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1258172	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258177	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258180	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258183	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258186	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1258175	AGAP6	cis	lung	GTEx
rs1258175	AGAP6	cis	Esophagus Mucosa	GTEx
rs1258175	AGAP6	cis	Thyroid	GTEx
rs1258175	AGAP6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50940600-50966000	Strong transcription	Liver	Liver
2	chr10:50941200-50965400	Weak transcription	Brain Germinal Matrix	brain
3	chr10:50943200-50969400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr10:50944000-50969400	Weak transcription	Brain Substantia Nigra	brain
5	chr10:50947800-50960400	Strong transcription	Brain Angular Gyrus	brain
6	chr10:50951600-50969200	Weak transcription	Fetal Intestine Large	intestine
7	chr10:50952600-50968800	Weak transcription	Pancreas	Pancrea
8	chr10:50953400-50969400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr10:50954400-50962400	Weak transcription	Brain Hippocampus Middle	brain
10	chr10:50954600-50958200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr10:50954800-50959400	Weak transcription	Right Atrium	heart
12	chr10:50955000-50958600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr10:50955000-50967800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr10:50955000-50969000	Weak transcription	Ovary	ovary
15	chr10:50955000-50969400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr10:50955200-50964200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr10:50955400-50958800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr10:50955400-50959600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:50955400-50960200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:50955600-50957400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr10:50955600-50957600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:50955600-50957600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:50955600-50957600	Weak transcription	Fetal Intestine Small	intestine
24	chr10:50955600-50958000	Weak transcription	Spleen	Spleen
25	chr10:50955600-50958400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr10:50955600-50959400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr10:50956200-50957400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:50956200-50958600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr10:50956400-50957200	Weak transcription	Brain Anterior Caudate	brain
30	chr10:50956600-50957000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr10:50956600-50957200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr10:50956600-50958400	Weak transcription	Brain Inferior Temporal Lobe	brain

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