Variant report

Variant	rs11804236
Chromosome Location	chr1:179335960-179335961
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	MXI1	chr1:179334503-179336055	SK-N-SH	brain:	n/a	chr1:179335077-179335092

No.	Distal block	Cell Line	Cell type
1	chr1:179198544..179200421-chr1:179334252..179336417,2	MCF-7	breast:
2	chr1:179332952..179336574-chr1:179337996..179342859,7	MCF-7	breast:
3	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
4	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:
5	chr1:179048972..179052099-chr1:179331450..179336701,5	MCF-7	breast:
6	chr1:179333390..179336673-chr1:179338029..179341473,3	MCF-7	breast:

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

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11577489	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11581507	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11799784	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11804234	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13306727	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13306730	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16853998	0.98[EUR][1000 genomes]
rs17369088	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2152320	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2184575	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45471092	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4651024	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4652366	0.95[ASN][1000 genomes]
rs55906130	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs55986478	0.98[EUR][1000 genomes]
rs56149964	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56303406	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57864135	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6425534	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6673354	0.81[EUR][1000 genomes]
rs6682068	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67545145	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68098532	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525946	0.81[EUR][1000 genomes]
rs7534976	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11804236	TDRD5	cis	Artery Aorta	GTEx
rs11804236	TDRD5	cis	Artery Tibial	GTEx
rs11804236	TDRD5	cis	Esophagus Mucosa	GTEx
rs11804236	TDRD5	cis	Thyroid	GTEx
rs11804236	SOAT1	cis	Whole Blood	GTEx
rs11804236	AXDND1	cis	Nerve Tibial	GTEx
rs11804236	TDRD5	cis	Nerve Tibial	GTEx
rs11804236	AXDND1	cis	Thyroid	GTEx
rs11804236	TDRD5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:37 , 50 per page) page: 1

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	chr1:179334200-179336000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr1:179334200-179336000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:179334200-179336000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:179334400-179336000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:179334400-179336000	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:179334400-179336000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:179334400-179336000	Active TSS	NHDF-Ad	bronchial
10	chr1:179334600-179336000	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:179334600-179336000	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr1:179334600-179336000	Active TSS	Muscle Satellite Cultured Cells	--
13	chr1:179335200-179336000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr1:179335200-179336000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:179335200-179336000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr1:179335400-179336000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:179335400-179336000	Active TSS	HepG2	liver
18	chr1:179335600-179336000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:179335600-179336000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:179335800-179336000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr1:179335800-179336000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:179335800-179336000	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr1:179335800-179336000	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:179335800-179336000	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:179335800-179336000	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:179335800-179336000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr1:179335800-179336000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:179335800-179336000	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr1:179335800-179336000	Enhancers	Duodenum Mucosa	Duodenum
30	chr1:179335800-179336000	Enhancers	Fetal Brain Female	brain
31	chr1:179335800-179336000	Enhancers	Fetal Intestine Large	intestine
32	chr1:179335800-179336000	Active TSS	Rectal Smooth Muscle	rectum
33	chr1:179335800-179336000	Enhancers	Dnd41	blood
34	chr1:179335800-179336000	Enhancers	Hela-S3	cervix
35	chr1:179335800-179336000	Active TSS	HMEC	breast
36	chr1:179335800-179336000	Enhancers	Osteobl	bone
37	chr1:179335800-179336400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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