Variant report

Variant	rs1999068
Chromosome Location	chr1:179560718-179560719
allele	A/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	MAX	chr1:179560449-179561784	MCF-7	breast:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
2	MAX	chr1:179560515-179561699	H1-hESC	embryonic stem cell:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
3	EP300	chr1:179560599-179561400	MCF-7	breast:	n/a	chr1:179560975-179560984 chr1:179561035-179561051 chr1:179561091-179561107 chr1:179560814-179560830 chr1:179560818-179560834 chr1:179560965-179560981
4	ESR1	chr1:179560706-179560992	T-47D	breast:	n/a	n/a
5	TEAD4	chr1:179560689-179561190	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:179560689-179560805	MCF-7	breast:	n/a	n/a
7	CTCF	chr1:179560615-179561099	T-47D	breast:	n/a	n/a
8	MAX	chr1:179560468-179561767	H1-hESC	embryonic stem cell:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
9	E2F6	chr1:179560348-179561861	H1-hESC	embryonic stem cell:	n/a	chr1:179560963-179560972 chr1:179561264-179561273 chr1:179561352-179561359
10	NR2F2	chr1:179560573-179561479	MCF-7	breast:	n/a	n/a
11	MAX	chr1:179560583-179561357	A549	lung:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
12	CTCF	chr1:179560698-179560802	MCF-7	breast:	n/a	n/a
13	MAX	chr1:179560550-179561080	H1-hESC	embryonic stem cell:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
14	E2F6	chr1:179560670-179561151	A549	lung:	n/a	chr1:179560963-179560972
15	MAX	chr1:179560418-179561505	A549	lung:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
16	CTCF	chr1:179560716-179560795	MCF-7	breast:	n/a	n/a
17	EP300	chr1:179560654-179561197	T-47D	breast:	n/a	chr1:179560975-179560984 chr1:179561035-179561051 chr1:179561091-179561107 chr1:179560814-179560830 chr1:179560818-179560834 chr1:179560965-179560981
18	CTCF	chr1:179560640-179560790	HCM	heart:	n/a	n/a
19	GABPA	chr1:179560614-179561403	MCF-7	breast:	n/a	chr1:179560962-179560976 chr1:179560962-179560973 chr1:179560959-179560973 chr1:179560969-179560978 chr1:179560962-179560971
20	FOXA1	chr1:179560594-179561143	T-47D	breast:	n/a	n/a
21	RAD21	chr1:179560597-179561539	H1-hESC	embryonic stem cell:	n/a	n/a
22	USF1	chr1:179560634-179561150	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr1:179560364-179561745	MCF-7	breast:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
24	MAX	chr1:179560716-179561089	ECC-1	luminal epithelium:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
25	CREB1	chr1:179560520-179561044	A549	lung:	n/a	n/a
26	ZNF143	chr1:179560708-179561535	H1-hESC	embryonic stem cell:	n/a	chr1:179560951-179560961
27	CREB1	chr1:179560584-179561320	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr1:179560620-179560770	Caco-2	colon:	n/a	n/a
29	E2F6	chr1:179560548-179561684	H1-hESC	embryonic stem cell:	n/a	chr1:179560963-179560972 chr1:179561264-179561273 chr1:179561352-179561359
30	TEAD4	chr1:179560686-179561130	H1-hESC	embryonic stem cell:	n/a	n/a
31	MYC	chr1:179560506-179561069	MCF10A-Er-Src	breast:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
32	GATA3	chr1:179560467-179561629	MCF-7	breast:	n/a	n/a
33	POLR2A	chr1:179560694-179561295	MCF-7	breast:	n/a	n/a
34	POLR2A	chr1:179560492-179561164	MCF10A-Er-Src	breast:	n/a	n/a
35	E2F4	chr1:179560654-179560765	MCF10A-Er-Src	breast:	n/a	n/a
36	E2F6	chr1:179560476-179561313	A549	lung:	n/a	chr1:179560963-179560972 chr1:179561264-179561273
37	POLR2A	chr1:179560693-179561313	MCF-7	breast:	n/a	n/a
38	POLR2A	chr1:179560509-179561143	MCF10A-Er-Src	breast:	n/a	n/a
39	CTCF	chr1:179560539-179561629	MCF-7	breast:	n/a	chr1:179561092-179561105
40	TCF12	chr1:179560281-179561504	MCF-7	breast:	n/a	chr1:179561175-179561185
41	ELF1	chr1:179560552-179561672	MCF-7	breast:	n/a	chr1:179561099-179561111 chr1:179561384-179561393
42	HDAC2	chr1:179560417-179561728	MCF-7	breast:	n/a	n/a
43	MAX	chr1:179560649-179561068	K562	blood:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
44	BACH1	chr1:179560494-179560764	H1-hESC	embryonic stem cell:	n/a	n/a
45	E2F6	chr1:179560715-179561066	K562	blood:	n/a	chr1:179560963-179560972
46	SP4	chr1:179560699-179561132	H1-hESC	embryonic stem cell:	n/a	n/a
47	MYC	chr1:179560642-179561262	MCF-7	breast:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
48	MYC	chr1:179560467-179560926	MCF10A-Er-Src	breast:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
49	USF1	chr1:179560656-179561079	H1-hESC	embryonic stem cell:	n/a	n/a
50	TBP	chr1:179560709-179561426	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:179560700-179560750	HL-60	blood:	n/a
2	chr1:179560700-179560750	ovcar-3	ovarian:	n/a
3	chr1:179560700-179560750	Jurkat	blood:	n/a
4	chr1:179560700-179560750	SK-N-MC	brain:	n/a
5	chr1:179560700-179560750	K562	blood:	n/a
6	chr1:179560700-179560750	HCPEpiC	choroid plexus:	n/a
7	chr1:179560700-179560750	HRCEpiC	kidney:	n/a
8	chr1:179560700-179560750	HNPCEpiC	eye:	n/a
9	chr1:179560700-179560750	SK-N-SH_RA	brain:	n/a
10	chr1:179560700-179560750	HCF	heart:	n/a
11	chr1:179560700-179560750	Hepatocyte	liver:	n/a
12	chr1:179560700-179560750	ECC-1	luminal epithelium:	n/a
13	chr1:179560700-179560750	AG10803	skin:	n/a
14	chr1:179560700-179560750	SK-N-SH	brain:	n/a
15	chr1:179560700-179560750	NHDF-neo	bronchial:	n/a
16	chr1:179560700-179560750	Caco-2	colon:	n/a
17	chr1:179560700-179560750	U87	brain:	n/a
18	chr1:179560700-179560750	HCT-116	colon:	n/a
19	chr1:179560700-179560750	T-47D	breast:	n/a
20	chr1:179560700-179560750	MCF-7	breast:	n/a
21	chr1:179560700-179560750	NB4	blood:	n/a
22	chr1:179560700-179560750	LNCaP	prostate:	n/a
23	chr1:179560700-179560750	HAEpiC	amniotic membrane:	n/a
24	chr1:179560700-179560750	SAEC	small airway:	n/a
25	chr1:179560700-179560750	Hela-S3	cervix:	n/a
26	chr1:179560700-179560750	PANC-1	pancreas:	n/a
27	chr1:179560700-179560750	HMEC	breast:	n/a
28	chr1:179560700-179560750	HCM	heart:	n/a
29	chr1:179560700-179560750	AG09319	gingival:	n/a
30	chr1:179560700-179560750	GM19239	blood:	n/a
31	chr1:179560700-179560750	SKMC	muscle:	n/a
32	chr1:179560700-179560750	HIPEpiC	eye:	n/a
33	chr1:179560700-179560750	HPAEpiC	pulmonary alveolar:	n/a
34	chr1:179560700-179560750	IMR90	lung:	fetal
35	chr1:179560700-179560750	ProgFib	skin:	n/a
36	chr1:179560700-179560750	MCF10A-Er-Src	breast:	n/a
37	chr1:179560700-179560750	GM06990	blood:	n/a
38	chr1:179560700-179560750	AG04450	lung:	fetal
39	chr1:179560700-179560750	PrEC	prostate:	n/a
40	chr1:179560700-179560750	HUVEC	blood vessel:	n/a
41	chr1:179560700-179560750	HRE	kidney:	n/a
42	chr1:179560700-179560750	GM12891	blood:	n/a
43	chr1:179560700-179560750	PFSK-1	brain:	n/a
44	chr1:179560700-179560750	H1-hESC	embryonic stem cell:	embryo
45	chr1:179560700-179560750	NT2-D1	testis:	n/a
46	chr1:179560700-179560750	HRPEpiC	eye:	n/a
47	chr1:179560700-179560750	A549	lung:	n/a
48	chr1:179560700-179560750	BE2_C	brain:	n/a
49	chr1:179560700-179560750	AoSMC	blood vessel:	n/a
50	chr1:179560700-179560750	AG04449	skin:	fetal

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179553040..179558877-chr1:179559940..179564416,7	MCF-7	breast:

Variant related genes	Relation type
TDRD5	TF binding region
TDRD5	CpG island
ENSG00000227141	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10157829	0.88[ASN][1000 genomes]
rs1079291	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11577538	0.83[EUR][1000 genomes]
rs11586725	0.83[EUR][1000 genomes]
rs12021675	0.85[ASN][1000 genomes]
rs12035247	0.82[ASN][1000 genomes]
rs12042409	0.82[ASN][1000 genomes]
rs12045588	0.81[ASN][1000 genomes]
rs2274622	0.84[EUR][1000 genomes]
rs3765547	0.86[ASN][1000 genomes]
rs4474210	0.85[ASN][1000 genomes]
rs4520380	0.82[ASN][1000 genomes]
rs55635521	0.94[ASN][1000 genomes]
rs58593782	0.82[ASN][1000 genomes]
rs61310274	0.94[ASN][1000 genomes]
rs6425588	0.82[ASN][1000 genomes]
rs6689426	0.94[ASN][1000 genomes]
rs6691856	0.82[ASN][1000 genomes]
rs6692069	0.82[ASN][1000 genomes]
rs74132225	0.82[ASN][1000 genomes]
rs744446	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7519700	0.83[EUR][1000 genomes]
rs7520355	0.82[ASN][1000 genomes]
rs7541890	0.83[EUR][1000 genomes]
rs7541899	0.83[EUR][1000 genomes]
rs7547484	0.82[ASN][1000 genomes]
rs7547988	0.82[ASN][1000 genomes]
rs913514	0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3424735	chr1:179559954-179562502	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1999068	TDRD5	cis	thalamus	BrainEAC
rs1999068	TDRD5	cis	Esophagus Mucosa	GTEx
rs1999068	TDRD5	cis	brain	BrainEAC
rs1999068	TDRD5	cis	Nerve Tibial	GTEx
rs1999068	TDRD5	cis	Adipose Subcutaneous	GTEx
rs1999068	TDRD5	cis	Artery Aorta	GTEx
rs1999068	TDRD5	cis	lung	GTEx
rs1999068	RP11-545A16.3	cis	Artery Aorta	GTEx
rs1999068	TDRD5	cis	frontal cortex	BrainEAC
rs1999068	TDRD5	cis	Thyroid	GTEx
rs1999068	TDRD5	cis	temporal cortex	BrainEAC
rs1999068	TDRD5	cis	Artery Tibial	GTEx
rs1999068	TDRD5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179560400-179560800	Enhancers	Stomach Mucosa	stomach
2	chr1:179560400-179561000	Active TSS	Duodenum Mucosa	Duodenum
3	chr1:179560400-179561000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr1:179560400-179561400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:179560400-179561400	Bivalent Enhancer	Fetal Brain Male	brain
6	chr1:179560600-179560800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:179560600-179560800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:179560600-179560800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:179560600-179560800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:179560600-179560800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:179560600-179560800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:179560600-179560800	Bivalent Enhancer	Brain Hippocampus Middle	brain
13	chr1:179560600-179560800	Active TSS	Colonic Mucosa	Colon
14	chr1:179560600-179560800	Bivalent Enhancer	Esophagus	oesophagus
15	chr1:179560600-179560800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
16	chr1:179560600-179560800	Flanking Bivalent TSS/Enh	Placenta	Placenta
17	chr1:179560600-179560800	Enhancers	Gastric	stomach
18	chr1:179560600-179560800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr1:179560600-179560800	Bivalent Enhancer	Right Ventricle	heart
20	chr1:179560600-179560800	Active TSS	A549	lung
21	chr1:179560600-179560800	Bivalent Enhancer	HMEC	breast
22	chr1:179560600-179560800	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
23	chr1:179560600-179561000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
24	chr1:179560600-179561000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:179560600-179561000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr1:179560600-179561000	Flanking Active TSS	Right Atrium	heart
27	chr1:179560600-179561000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
28	chr1:179560600-179561200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
29	chr1:179560600-179561200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:179560600-179561200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
31	chr1:179560600-179561200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:179560600-179561200	Bivalent/Poised TSS	Fetal Stomach	stomach
33	chr1:179560600-179561200	Flanking Active TSS	Pancreas	Pancrea
34	chr1:179560600-179561200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
35	chr1:179560600-179561200	Bivalent/Poised TSS	NHEK	skin
36	chr1:179560600-179561400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:179560600-179561400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:179560600-179561400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:179560600-179561400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:179560600-179561400	Active TSS	Brain Anterior Caudate	brain
41	chr1:179560600-179561400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
42	chr1:179560600-179561400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
43	chr1:179560600-179561400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
44	chr1:179560600-179561400	Bivalent/Poised TSS	Fetal Brain Female	brain
45	chr1:179560600-179561400	Bivalent Enhancer	Fetal Heart	heart
46	chr1:179560600-179561400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr1:179560600-179561400	Bivalent Enhancer	Spleen	Spleen
48	chr1:179560600-179561600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
49	chr1:179560600-179562000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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