Variant report

Variant	rs10875682
Chromosome Location	chr12:48083709-48083710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48082467..48084685-chr12:48086429..48089093,4	K562	blood:
2	chr12:48082326..48084499-chr12:48098211..48100235,2	MCF-7	breast:
3	chr12:48082733..48084619-chr12:48086537..48089093,2	K562	blood:

Variant related genes	Relation type
ENSG00000257433	Chromatin interaction
ENSG00000005175	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10783212	0.97[ASN][1000 genomes]
rs10875677	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875685	0.80[ASN][1000 genomes]
rs10875686	0.83[ASN][1000 genomes]
rs10875687	0.81[ASN][1000 genomes]
rs10875688	0.81[ASN][1000 genomes]
rs11168191	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168192	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168193	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168199	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168200	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168203	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168208	0.87[ASN][1000 genomes]
rs11168214	0.81[ASN][1000 genomes]
rs11168215	0.81[ASN][1000 genomes]
rs11168216	0.81[ASN][1000 genomes]
rs12366410	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12367193	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12370643	0.92[ASN][1000 genomes]
rs1541384	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072117	0.81[ASN][1000 genomes]
rs2240079	0.81[ASN][1000 genomes]
rs2240080	0.81[ASN][1000 genomes]
rs2283346	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764013	0.86[ASN][1000 genomes]
rs56011001	0.81[EUR][1000 genomes]
rs56240307	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582680	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs583752	0.84[EUR][1000 genomes]
rs602143	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs604662	0.82[EUR][1000 genomes]
rs605499	0.83[EUR][1000 genomes]
rs612773	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61917590	0.91[ASN][1000 genomes]
rs61917591	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61917594	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61917595	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61917616	0.81[ASN][1000 genomes]
rs61917617	0.81[ASN][1000 genomes]
rs622098	0.84[EUR][1000 genomes]
rs623894	0.84[EUR][1000 genomes]
rs630777	0.91[ASN][1000 genomes]
rs632944	0.91[ASN][1000 genomes]
rs634833	0.83[EUR][1000 genomes]
rs642453	0.81[EUR][1000 genomes]
rs644531	0.83[EUR][1000 genomes]
rs646223	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs652380	0.84[EUR][1000 genomes]
rs653136	0.82[EUR][1000 genomes]
rs6580634	0.96[ASN][1000 genomes]
rs658567	0.83[EUR][1000 genomes]
rs659836	0.83[EUR][1000 genomes]
rs668968	0.83[EUR][1000 genomes]
rs671961	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs687676	0.82[EUR][1000 genomes]
rs7136561	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7137529	0.92[ASN][1000 genomes]
rs7311663	0.97[ASN][1000 genomes]
rs7316761	0.82[EUR][1000 genomes]
rs7484827	0.81[ASN][1000 genomes]
rs7954502	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7969186	0.88[ASN][1000 genomes]
rs7976748	0.87[ASN][1000 genomes]
rs7977613	0.97[ASN][1000 genomes]
rs7977786	0.84[EUR][1000 genomes]
rs864112	0.82[EUR][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	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
2	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv695	chr12:48043261-48088221	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10875682	ENDOU	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48029800-48098800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:48040600-48086000	Weak transcription	Fetal Brain Male	brain
3	chr12:48046600-48087800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:48046600-48090000	Weak transcription	Psoas Muscle	Psoas
5	chr12:48046600-48097000	Weak transcription	Brain Angular Gyrus	brain
6	chr12:48046600-48097600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:48046600-48099200	Weak transcription	Gastric	stomach
8	chr12:48046800-48098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:48046800-48099000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:48050200-48098600	Weak transcription	Pancreas	Pancrea
11	chr12:48052000-48094400	Weak transcription	Aorta	Aorta
12	chr12:48056000-48099000	Weak transcription	Right Ventricle	heart
13	chr12:48057200-48098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:48058000-48098600	Weak transcription	Colonic Mucosa	Colon
15	chr12:48058200-48086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:48058800-48086000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:48060400-48088400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:48060600-48084200	Weak transcription	Thymus	Thymus
19	chr12:48060600-48086000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:48060600-48094200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:48060800-48094200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:48061600-48088600	Weak transcription	Brain Substantia Nigra	brain
23	chr12:48062600-48094200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:48062800-48098600	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:48063000-48086400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:48063000-48099000	Weak transcription	Small Intestine	intestine
27	chr12:48064600-48086000	Weak transcription	Lung	lung
28	chr12:48064600-48086000	Weak transcription	HSMMtube	muscle
29	chr12:48064600-48099200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:48064800-48089600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:48064800-48090000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:48065000-48092800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:48066400-48086000	Weak transcription	Fetal Heart	heart
34	chr12:48068400-48097200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:48071800-48091600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:48072800-48086000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:48072800-48090200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:48072800-48091400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:48072800-48091600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:48073000-48091800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:48073200-48086600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:48073600-48091200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr12:48074000-48093600	Weak transcription	HMEC	breast
44	chr12:48074000-48095400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:48074000-48095800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:48074200-48097000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:48074200-48099000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr12:48075000-48086000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:48075400-48085200	Weak transcription	Fetal Kidney	kidney
50	chr12:48075400-48085800	Weak transcription	Rectal Mucosa Donor 29	rectum

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