Variant report

Variant	rs500905
Chromosome Location	chr1:67218004-67218005
allele	C/G
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	CHD1	chr1:67217825-67218252	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:67217710-67218137	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr1:67217920-67218070	GM12873	blood:	n/a	chr1:67218011-67218029
4	CTCF	chr1:67217980-67218130	GM12867	blood:	n/a	chr1:67218011-67218029
5	CTCF	chr1:67217917-67218119	H1-hESC	embryonic stem cell:	n/a	chr1:67218011-67218029
6	CTCF	chr1:67217880-67218030	HAc	cerebellar:	n/a	chr1:67218011-67218029
7	CTCF	chr1:67217880-67218030	AoAF	blood vessel:	n/a	chr1:67218011-67218029
8	CTCF	chr1:67217960-67218110	HCFaa	heart:	n/a	chr1:67218011-67218029
9	MAX	chr1:67217585-67218316	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr1:67217900-67218050	HPF	lung:	n/a	chr1:67218011-67218029
11	CTCF	chr1:67217909-67218138	ProgFib	skin:	n/a	chr1:67218011-67218029
12	CTCF	chr1:67217940-67218090	AG04449	skin:	n/a	chr1:67218011-67218029
13	JUND	chr1:67217759-67218137	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr1:67217960-67218110	HCPEpiC	choroid plexus:	n/a	chr1:67218011-67218029
15	CTCF	chr1:67217940-67218090	AG04450	lung:	n/a	chr1:67218011-67218029
16	SIN3A	chr1:67217804-67218361	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZNF143	chr1:67217710-67218295	H1-hESC	embryonic stem cell:	n/a	chr1:67218176-67218195
18	CTCF	chr1:67217904-67218107	NHEK	skin:	n/a	chr1:67218011-67218029
19	CTCF	chr1:67217980-67218130	HL-60	blood:	n/a	chr1:67218011-67218029
20	CTCF	chr1:67217964-67218035	GM10248	blood:	n/a	chr1:67218011-67218029
21	CTCF	chr1:67217943-67218108	GM10266	blood:	n/a	chr1:67218011-67218029
22	CTCF	chr1:67217900-67218050	AG10803	skin:	n/a	chr1:67218011-67218029
23	CTCF	chr1:67217875-67218159	Fibrobl	skin:	n/a	chr1:67218011-67218029
24	CTCF	chr1:67217900-67218050	HPAF	blood vessel:	n/a	chr1:67218011-67218029
25	CTCF	chr1:67217960-67218110	AG09319	gingival:	n/a	chr1:67218011-67218029
26	CTCF	chr1:67217900-67218050	HFF-Myc	foreskin:	n/a	chr1:67218011-67218029
27	CTCF	chr1:67217940-67218090	AG09319	gingival:	n/a	chr1:67218011-67218029
28	CTCF	chr1:67217860-67218010	GM12867	blood:	n/a	n/a
29	CTCF	chr1:67217960-67218110	HA-sp	spinal cord:	n/a	chr1:67218011-67218029
30	CTCF	chr1:67217920-67218070	HUVEC	blood vessel:	n/a	chr1:67218011-67218029
31	GATA2	chr1:67217653-67218086	HUVEC	blood vessel:	n/a	n/a
32	CTCF	chr1:67217923-67218097	Lung_OC	lung:	n/a	chr1:67218011-67218029
33	CTCF	chr1:67217960-67218110	GM12871	blood:	n/a	chr1:67218011-67218029
34	POLR2A	chr1:67217588-67218241	HUVEC	blood vessel:	n/a	n/a
35	CTCF	chr1:67217918-67218127	Gliobla	brain:	n/a	chr1:67218011-67218029
36	CTCF	chr1:67217793-67218139	H1-hESC	embryonic stem cell:	n/a	chr1:67218011-67218029
37	POLR2A	chr1:67217640-67218046	ProgFib	skin:	n/a	n/a
38	POLR2A	chr1:67217678-67218632	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr1:67217987-67218122	GM13977	blood:	n/a	chr1:67218011-67218029
40	CTCF	chr1:67217980-67218130	GM12865	blood:	n/a	chr1:67218011-67218029
41	POLR2A	chr1:67217595-67218335	HUVEC	blood vessel:	n/a	n/a
42	CTCF	chr1:67217870-67218121	H1-hESC	embryonic stem cell:	n/a	chr1:67218011-67218029
43	RAD21	chr1:67217909-67218085	GM12878	blood:	n/a	chr1:67218020-67218032 chr1:67218009-67218028
44	E2F6	chr1:67217534-67218417	H1-hESC	embryonic stem cell:	n/a	chr1:67217885-67217892 chr1:67217885-67217892 chr1:67217885-67217892
45	TBP	chr1:67217629-67218506	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr1:67217920-67218070	HBMEC	blood vessel:	n/a	chr1:67218011-67218029
47	CTCF	chr1:67217920-67218070	NHDF-neo	bronchial:	n/a	chr1:67218011-67218029
48	CTCF	chr1:67217920-67218070	AG10803	skin:	n/a	chr1:67218011-67218029
49	TAF1	chr1:67217885-67218359	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr1:67217908-67218145	GM12891	blood:	n/a	chr1:67218011-67218029

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:67217984-67218034	H1-hESC	embryonic stem cell:	embryo
2	chr1:67217984-67218034	Caco-2	colon:	n/a
3	chr1:67217984-67218034	Jurkat	blood:	n/a
4	chr1:67217984-67218034	HCT-116	colon:	n/a
5	chr1:67217984-67218034	HUVEC	blood vessel:	n/a
6	chr1:67217984-67218034	AG10803	skin:	n/a
7	chr1:67217984-67218034	AG04450	lung:	fetal
8	chr1:67217984-67218034	SK-N-MC	brain:	n/a
9	chr1:67217984-67218034	Hepatocyte	liver:	n/a
10	chr1:67217984-67218034	PrEC	prostate:	n/a
11	chr1:67217984-67218034	IMR90	lung:	fetal
12	chr1:67217984-67218034	AG04449	skin:	fetal
13	chr1:67217984-67218034	NB4	blood:	n/a
14	chr1:67217984-67218034	SK-N-SH_RA	brain:	n/a
15	chr1:67217984-67218034	GM12891	blood:	n/a
16	chr1:67217984-67218034	HAEpiC	amniotic membrane:	n/a
17	chr1:67217984-67218034	HEK293	kidney:	embryo
18	chr1:67217984-67218034	CMK	blood:	n/a
19	chr1:67217984-67218034	MCF-7	breast:	n/a
20	chr1:67217984-67218034	ECC-1	luminal epithelium:	n/a
21	chr1:67217984-67218034	HCF	heart:	n/a
22	chr1:67217984-67218034	HepG2	liver:	n/a
23	chr1:67217984-67218034	HNPCEpiC	eye:	n/a
24	chr1:67217984-67218034	HIPEpiC	eye:	n/a
25	chr1:67217984-67218034	SAEC	small airway:	n/a
26	chr1:67217984-67218034	K562	blood:	n/a
27	chr1:67217984-67218034	Hela-S3	cervix:	n/a
28	chr1:67217984-67218034	U87	brain:	n/a
29	chr1:67217984-67218034	GM12878	blood:	n/a
30	chr1:67217984-67218034	NHDF-neo	bronchial:	n/a
31	chr1:67217984-67218034	AoSMC	blood vessel:	n/a
32	chr1:67217984-67218034	NHBE	bronchial:	n/a
33	chr1:67217984-67218034	HCPEpiC	choroid plexus:	n/a
34	chr1:67217984-67218034	BE2_C	brain:	n/a
35	chr1:67217984-67218034	A549	lung:	n/a
36	chr1:67217984-67218034	AG09309	skin:	n/a
37	chr1:67217984-67218034	GM12892	blood:	n/a
38	chr1:67217984-67218034	HMEC	breast:	n/a
39	chr1:67217984-67218034	ProgFib	skin:	n/a
40	chr1:67217984-67218034	NT2-D1	testis:	n/a
41	chr1:67217984-67218034	GM19239	blood:	n/a
42	chr1:67217984-67218034	HEEpiC	esophagus:	n/a
43	chr1:67217984-67218034	HL-60	blood:	n/a
44	chr1:67217984-67218034	SKMC	muscle:	n/a
45	chr1:67217984-67218034	ovcar-3	ovarian:	n/a
46	chr1:67217984-67218034	MCF10A-Er-Src	breast:	n/a
47	chr1:67217984-67218034	LNCaP	prostate:	n/a
48	chr1:67217984-67218034	HPAEpiC	pulmonary alveolar:	n/a
49	chr1:67217984-67218034	RPTEC	kidney:	n/a
50	chr1:67217984-67218034	BJ	skin:	n/a

Variant related genes	Relation type
TCTEX1D1	TF binding region
TCTEX1D1	CpG island

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11811067	0.86[ASN][1000 genomes]
rs12119578	0.85[ASN][1000 genomes]
rs12138266	0.83[ASN][1000 genomes]
rs1280309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016093	0.96[ASN][1000 genomes]
rs2274987	0.93[ASN][1000 genomes]
rs473470	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs485122	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs487833	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs512691	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs523544	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs524204	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs531386	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538659	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs553729	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs562348	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609906	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs609939	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs610295	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs624277	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs630410	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657808	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663604	0.96[ASN][1000 genomes]
rs6679379	0.82[ASN][1000 genomes]
rs678253	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs693956	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541249	0.94[ASN][1000 genomes]
rs9988481	0.82[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
rs500905	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67217200-67218400	Active TSS	Brain Angular Gyrus	brain
2	chr1:67217200-67218600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:67217200-67218800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:67217200-67219000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr1:67217200-67219200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr1:67217200-67220400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:67217200-67220800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:67217400-67218600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
9	chr1:67217400-67218800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr1:67217400-67218800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:67217400-67218800	Enhancers	Spleen	Spleen
12	chr1:67217400-67219000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr1:67217600-67218200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr1:67217600-67218200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
15	chr1:67217600-67218400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:67217600-67218400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:67217600-67218400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:67217600-67218400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:67217600-67218400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:67217600-67218400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
21	chr1:67217600-67218400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
22	chr1:67217600-67218400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:67217600-67218400	Active TSS	Brain Hippocampus Middle	brain
24	chr1:67217600-67218400	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr1:67217600-67218400	Active TSS	Brain Substantia Nigra	brain
26	chr1:67217600-67218400	Active TSS	Colon Smooth Muscle	Colon
27	chr1:67217600-67218400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:67217600-67218400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
29	chr1:67217600-67218400	Active TSS	HSMMtube	muscle
30	chr1:67217600-67218400	Active TSS	NH-A	brain
31	chr1:67217600-67218400	Active TSS	NHLF	lung
32	chr1:67217600-67218600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:67217600-67218600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr1:67217600-67218600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:67217600-67218600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:67217600-67218600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:67217600-67218600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:67217600-67218600	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr1:67217600-67218600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr1:67217600-67218800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:67217600-67218800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:67217600-67218800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr1:67217600-67218800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:67217600-67219000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:67217600-67219000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr1:67217600-67219000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:67217600-67219000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:67217600-67219000	Flanking Active TSS	HUVEC	blood vessel
49	chr1:67217800-67218200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
50	chr1:67217800-67218200	Active TSS	Brain Cingulate Gyrus	brain

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