Variant report

Variant	rs11804234
Chromosome Location	chr1:179335952-179335953
allele	A/C
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
ENSG00000057252	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000162779	Chromatin interaction
ENSG00000143322	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10913736	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11577489	0.94[ASN][1000 genomes]
rs11581507	0.94[ASN][1000 genomes]
rs11799784	1.00[ASN][1000 genomes]
rs11804236	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16853998	0.95[ASN][1000 genomes]
rs16854003	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652366	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs55906130	0.95[ASN][1000 genomes]
rs55986478	0.95[ASN][1000 genomes]
rs57864135	0.96[ASN][1000 genomes]
rs6682068	0.85[EUR][1000 genomes]
rs68098532	0.91[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11804234	AXDND1	cis	Thyroid	GTEx
rs11804234	AXDND1	cis	Nerve Tibial	GTEx
rs11804234	TDRD5	cis	Artery Aorta	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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