Variant report

Variant	rs55771540
Chromosome Location	chr1:67202107-67202108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11811067	0.87[ASN][1000 genomes]
rs12119578	0.88[ASN][1000 genomes]
rs12138266	0.86[ASN][1000 genomes]
rs473470	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs485122	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs487833	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs512691	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs523544	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs524204	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs538659	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs553729	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs562348	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs609906	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs609939	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs610295	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs624277	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs657808	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6679379	0.84[ASN][1000 genomes]
rs678253	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs693956	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9988481	0.85[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	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
3	esv3429399	chr1:67200514-67202512	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55771540	TCTEX1D1	cis	lung	GTEx
rs55771540	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:31 , 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	chr1:67186400-67205000	Weak transcription	Fetal Heart	heart
4	chr1:67188600-67217400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:67191800-67204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:67191800-67204800	Weak transcription	Lung	lung
7	chr1:67192000-67204600	Weak transcription	Aorta	Aorta
8	chr1:67192000-67204800	Weak transcription	Left Ventricle	heart
9	chr1:67192000-67217200	Weak transcription	Brain Angular Gyrus	brain
10	chr1:67192000-67217400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:67192200-67204600	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:67192200-67208200	Weak transcription	Brain Substantia Nigra	brain
13	chr1:67192400-67204200	Weak transcription	Brain Anterior Caudate	brain
14	chr1:67196600-67212800	Weak transcription	Fetal Brain Female	brain
15	chr1:67197000-67217600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:67197600-67204600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:67198200-67203800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:67199200-67204600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:67199600-67203000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:67199600-67203600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:67199600-67204000	Weak transcription	NHDF-Ad	bronchial
22	chr1:67199600-67204800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:67199600-67205000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:67199600-67205200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:67199600-67205600	Weak transcription	NHLF	lung
26	chr1:67199600-67206400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:67199800-67205000	Weak transcription	Dnd41	blood
28	chr1:67199800-67205000	Weak transcription	Osteobl	bone
29	chr1:67201200-67203000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:67201200-67203400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:67201200-67203600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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