Variant report

Variant	rs11577489
Chromosome Location	chr1:179335162-179335163
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:437)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:437 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr1:179334966-179335251	K562	blood:	n/a	n/a
2	YY1	chr1:179334715-179335438	K562	blood:	n/a	n/a
3	MAX	chr1:179334645-179335560	NB4	blood:	n/a	n/a
4	POLR2A	chr1:179334536-179335456	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:179334667-179335241	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:179334702-179335693	IMR90	lung:	n/a	n/a
7	POLR2A	chr1:179334655-179335510	MCF10A-Er-Src	breast:	n/a	n/a
8	MAX	chr1:179334624-179335261	K562	blood:	n/a	n/a
9	POLR2A	chr1:179334625-179335326	HepG2	liver:	n/a	n/a
10	ELF1	chr1:179334702-179335377	HepG2	liver:	n/a	chr1:179335021-179335033
11	CTCF	chr1:179335160-179335310	GM12865	blood:	n/a	chr1:179335300-179335309
12	BCL3	chr1:179334455-179335348	A549	lung:	n/a	n/a
13	YY1	chr1:179334795-179335329	ECC-1	luminal epithelium:	n/a	n/a
14	SP1	chr1:179334509-179335371	A549	lung:	n/a	n/a
15	GATA3	chr1:179334730-179335325	T-47D	breast:	n/a	n/a
16	ATF2	chr1:179334685-179335334	GM12878	blood:	n/a	n/a
17	EGR1	chr1:179334652-179335382	MCF-7	breast:	n/a	chr1:179334845-179334854
18	POLR2A	chr1:179334975-179335349	A549	lung:	n/a	n/a
19	POLR2A	chr1:179333806-179335727	GM12891	blood:	n/a	n/a
20	TAF1	chr1:179334468-179335374	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr1:179335002-179335263	HepG2	liver:	n/a	n/a
22	MYC	chr1:179334990-179335277	MCF-7	breast:	n/a	n/a
23	BCL3	chr1:179334664-179335199	A549	lung:	n/a	n/a
24	TBP	chr1:179334670-179335363	GM12878	blood:	n/a	n/a
25	EP300	chr1:179334670-179335252	GM12878	blood:	n/a	chr1:179334928-179334942
26	HMGN3	chr1:179334727-179335433	K562	blood:	n/a	n/a
27	RCOR1	chr1:179334802-179335382	Hela-S3	cervix:	n/a	n/a
28	CREB1	chr1:179334632-179335457	A549	lung:	n/a	n/a
29	ELF1	chr1:179334736-179335347	A549	lung:	n/a	chr1:179335021-179335033
30	MYC	chr1:179334942-179335282	MCF10A-Er-Src	breast:	n/a	n/a
31	TBL1XR1	chr1:179334770-179335497	K562	blood:	n/a	n/a
32	CTCF	chr1:179335140-179335290	HEK293	kidney:	n/a	n/a
33	E2F6	chr1:179334573-179335440	A549	lung:	n/a	chr1:179334842-179334852 chr1:179334845-179334854
34	MAZ	chr1:179334603-179335405	K562	blood:	n/a	n/a
35	SIN3AK20	chr1:179334990-179335492	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr1:179334644-179335583	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:179334807-179335373	U87	brain:	n/a	n/a
38	ZNF143	chr1:179334660-179335449	K562	blood:	n/a	chr1:179335018-179335028
39	STAT5A	chr1:179334843-179335489	GM12878	blood:	n/a	n/a
40	RCOR1	chr1:179334791-179335762	K562	blood:	n/a	n/a
41	ARID3A	chr1:179334879-179335197	K562	blood:	n/a	n/a
42	ELK1	chr1:179334793-179335487	GM12878	blood:	n/a	n/a
43	CTCF	chr1:179335040-179335190	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr1:179334392-179335548	GM12878	blood:	n/a	n/a
45	CHD2	chr1:179334742-179335402	GM12878	blood:	n/a	n/a
46	ELF1	chr1:179334679-179335462	MCF-7	breast:	n/a	chr1:179335021-179335033
47	ETS1	chr1:179334937-179335215	A549	lung:	n/a	n/a
48	POLR2A	chr1:179334595-179335403	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:179334661-179335359	K562	blood:	n/a	n/a
50	POLR2A	chr1:179334490-179335539	HUVEC	blood vessel:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179198544..179200421-chr1:179334252..179336417,2	MCF-7	breast:
2	chr1:179334985..179335587-chr8:134308823..134309369,2	Hela-S3	cervix:
3	chr1:179049160..179052033-chr1:179333339..179335895,3	K562	blood:
4	chr1:179332952..179336574-chr1:179337996..179342859,7	MCF-7	breast:
5	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
6	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:
7	chr1:179048972..179052099-chr1:179331450..179336701,5	MCF-7	breast:
8	chr1:179333390..179336673-chr1:179338029..179341473,3	MCF-7	breast:

No data

Variant related genes	Relation type
AXDND1	TF binding region
ENSG00000186283	Chromatin interaction
ENSG00000057252	Chromatin interaction
ENSG00000143322	Chromatin interaction
ENSG00000104419	Chromatin interaction
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10913736	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11581507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799784	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11804234	0.94[ASN][1000 genomes]
rs11804236	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs13306727	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs13306730	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs16853998	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16854003	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17369088	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2152320	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2184575	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs45471092	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4651024	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4652366	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55906130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55986478	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56149964	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56303406	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57864135	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425534	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6673354	0.80[EUR][1000 genomes]
rs6682068	0.80[EUR][1000 genomes]
rs67545145	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68098532	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7525946	0.82[EUR][1000 genomes]
rs7534976	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv33901	chr1:179328708-179344905	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11577489	TDRD5	cis	Artery Tibial	GTEx
rs11577489	TDRD5	cis	Artery Aorta	GTEx
rs11577489	TDRD5	cis	Nerve Tibial	GTEx
rs11577489	SOAT1	cis	Whole Blood	GTEx
rs11577489	AXDND1	cis	Thyroid	GTEx
rs11577489	AXDND1	cis	Nerve Tibial	GTEx
rs11577489	TDRD5	cis	Thyroid	GTEx
rs11577489	TDRD5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179334000-179336000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:179334000-179336000	Active TSS	GM12878-XiMat	blood
3	chr1:179334200-179335200	Active TSS	Placenta	Placenta
4	chr1:179334200-179335400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:179334200-179335400	Active TSS	Duodenum Mucosa	Duodenum
6	chr1:179334200-179335400	Active TSS	Rectal Smooth Muscle	rectum
7	chr1:179334200-179335400	Active TSS	HSMMtube	muscle
8	chr1:179334200-179335600	Active TSS	Colon Smooth Muscle	Colon
9	chr1:179334200-179335600	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr1:179334200-179335600	Active TSS	A549	lung
11	chr1:179334200-179335600	Active TSS	HSMM	muscle
12	chr1:179334200-179335800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:179334200-179335800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:179334200-179335800	Active TSS	Colonic Mucosa	Colon
15	chr1:179334200-179336000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:179334200-179336000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:179334200-179336000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:179334400-179335200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:179334400-179335200	Active TSS	HMEC	breast
20	chr1:179334400-179335200	Active TSS	Monocytes-CD14+_RO01746	blood
21	chr1:179334400-179335200	Active TSS	NHLF	lung
22	chr1:179334400-179335400	Active TSS	Aorta	Aorta
23	chr1:179334400-179335400	Active TSS	Liver	Liver
24	chr1:179334400-179335400	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr1:179334400-179335400	Active TSS	NH-A	brain
26	chr1:179334400-179335600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:179334400-179335600	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr1:179334400-179335600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:179334400-179335600	Active TSS	Primary T cells from cord blood	blood
30	chr1:179334400-179335600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:179334400-179335600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:179334400-179335600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:179334400-179335600	Active TSS	Adipose Nuclei	Adipose
34	chr1:179334400-179335600	Active TSS	Brain Hippocampus Middle	brain
35	chr1:179334400-179335600	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr1:179334400-179335600	Active TSS	Fetal Brain Female	brain
37	chr1:179334400-179335600	Active TSS	Fetal Kidney	kidney
38	chr1:179334400-179335600	Active TSS	Fetal Lung	lung
39	chr1:179334400-179335600	Active TSS	Fetal Stomach	stomach
40	chr1:179334400-179335600	Active TSS	Gastric	stomach
41	chr1:179334400-179335600	Active TSS	Ovary	ovary
42	chr1:179334400-179335600	Active TSS	Small Intestine	intestine
43	chr1:179334400-179335600	Active TSS	Stomach Mucosa	stomach
44	chr1:179334400-179335600	Active TSS	Hela-S3	cervix
45	chr1:179334400-179335600	Active TSS	NHEK	skin
46	chr1:179334400-179335600	Active TSS	Osteobl	bone
47	chr1:179334400-179335800	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:179334400-179335800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr1:179334400-179335800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:179334400-179335800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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