Variant report

Variant	rs485122
Chromosome Location	chr1:67198642-67198643
allele	C/T
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	FOS	chr1:67198103-67198882	HUVEC	blood vessel:	n/a	n/a
2	STAT3	chr1:67198451-67198857	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:67198469-67198774	MCF10A-Er-Src	breast:	n/a	n/a
4	MAFK	chr1:67198491-67198767	K562	blood:	n/a	chr1:67198583-67198594 chr1:67198578-67198593
5	STAT3	chr1:67198412-67198798	MCF10A-Er-Src	breast:	n/a	n/a
6	MAFK	chr1:67198193-67199009	IMR90	lung:	n/a	chr1:67198583-67198594 chr1:67198578-67198593
7	MYC	chr1:67198534-67198860	MCF10A-Er-Src	breast:	n/a	n/a
8	MAFK	chr1:67198413-67198753	HepG2	liver:	n/a	chr1:67198583-67198594 chr1:67198578-67198593
9	FOS	chr1:67198436-67198795	MCF10A-Er-Src	breast:	n/a	n/a
10	MAFK	chr1:67198453-67198697	HepG2	liver:	n/a	chr1:67198583-67198594 chr1:67198578-67198593
11	PBX3	chr1:67198137-67198783	SK-N-SH	brain:	n/a	n/a
12	GATA2	chr1:67198465-67198820	HUVEC	blood vessel:	n/a	n/a
13	FOS	chr1:67198327-67198840	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:67198149-67198861	MCF10A-Er-Src	breast:	n/a	n/a
15	MAFF	chr1:67198438-67198729	HepG2	liver:	n/a	chr1:67198577-67198595
16	MAFF	chr1:67198452-67198710	K562	blood:	n/a	chr1:67198577-67198595

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67195090..67196807-chr1:67198511..67200575,2	K562	blood:
2	chr1:67197999..67199929-chr1:67205946..67207947,2	K562	blood:

Variant related genes	Relation type
ENSG00000221655	TF binding region
ENSG00000221655	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10789216	0.83[ASN][1000 genomes]
rs10889647	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10889649	0.85[ASN][1000 genomes]
rs11208948	0.83[ASN][1000 genomes]
rs11208951	0.85[ASN][1000 genomes]
rs11811067	0.93[ASN][1000 genomes]
rs12043460	0.81[AMR][1000 genomes]
rs12063436	0.84[ASN][1000 genomes]
rs12119578	0.94[ASN][1000 genomes]
rs12138266	0.95[ASN][1000 genomes]
rs12402709	0.81[AMR][1000 genomes]
rs1280309	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1315210	0.82[ASN][1000 genomes]
rs1325268	0.83[ASN][1000 genomes]
rs1408852	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1498354	0.85[ASN][1000 genomes]
rs1547644	0.85[ASN][1000 genomes]
rs16844	0.83[ASN][1000 genomes]
rs2016093	0.82[ASN][1000 genomes]
rs2181625	0.85[ASN][1000 genomes]
rs2647386	0.88[AMR][1000 genomes]
rs35886191	0.82[AMR][1000 genomes]
rs3738167	0.85[ASN][1000 genomes]
rs473470	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs487833	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs489300	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs492358	0.81[AMR][1000 genomes]
rs500905	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs512691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523544	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs524204	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs531386	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs538659	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs553729	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55771540	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs562348	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609906	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs609939	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610295	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs624277	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs630410	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs650202	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs657808	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6659325	0.83[ASN][1000 genomes]
rs6663604	0.82[ASN][1000 genomes]
rs6679379	0.97[ASN][1000 genomes]
rs678253	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs682896	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs693956	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7512401	0.83[ASN][1000 genomes]
rs7541249	0.85[ASN][1000 genomes]
rs9988481	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv830093	chr1:67173594-67348264	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs485122	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
2	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
3	chr1:67184800-67199400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:67186400-67205000	Weak transcription	Fetal Heart	heart
5	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:67190200-67201200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:67191800-67204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:67191800-67204800	Weak transcription	Lung	lung
9	chr1:67192000-67204600	Weak transcription	Aorta	Aorta
10	chr1:67192000-67204800	Weak transcription	Left Ventricle	heart
11	chr1:67192000-67217200	Weak transcription	Brain Angular Gyrus	brain
12	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:67192200-67204600	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:67192200-67208200	Weak transcription	Brain Substantia Nigra	brain
15	chr1:67192400-67204200	Weak transcription	Brain Anterior Caudate	brain
16	chr1:67193000-67199600	Enhancers	Primary hematopoietic stem cells	blood
17	chr1:67193800-67199600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:67195400-67198800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:67195400-67199800	Enhancers	Dnd41	blood
20	chr1:67196600-67212800	Weak transcription	Fetal Brain Female	brain
21	chr1:67196800-67199800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:67197000-67201200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:67197000-67217600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:67197200-67199200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:67197200-67199600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr1:67197400-67199800	Enhancers	Osteobl	bone
27	chr1:67197600-67204600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:67197800-67199600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:67197800-67199600	Enhancers	HUVEC	blood vessel
30	chr1:67198000-67199000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:67198000-67199400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:67198000-67199600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:67198000-67199600	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr1:67198000-67199600	Enhancers	NHLF	lung
35	chr1:67198200-67199400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:67198200-67203800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:67198400-67199200	Genic enhancers	NHDF-Ad	bronchial
38	chr1:67198400-67199800	Enhancers	NHEK	skin
39	chr1:67198400-67200000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:67198600-67199200	Enhancers	Fetal Lung	lung
41	chr1:67198600-67199600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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