Variant report

Variant	rs11164117
Chromosome Location	chr2:95680267-95680268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95677663..95680622-chr2:95680904..95683785,2	K562	blood:
2	chr2:95651873..95654284-chr2:95678219..95680658,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17802697	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4096824	0.81[AMR][1000 genomes]
rs4443026	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67014278	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6709052	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6721123	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6723444	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6747563	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11164117	NMNAT2	trans	cerebellum	SCAN
rs11164117	ZNF514	Cis_1M	lymphoblastoid	RTeQTL
rs11164117	ZNF514	cis	parietal	SCAN
rs11164117	ZNF514	cis	Thyroid	GTEx
rs11164117	ZNF514	cis	Muscle Skeletal	GTEx
rs11164117	CYP4F32P	cis	Esophagus Mucosa	GTEx
rs11164117	ZNF514	cis	Whole Blood	GTEx
rs11164117	ZNF514	cis	cerebellum	SCAN
rs11164117	ACTR1B	cis	cerebellum	SCAN
rs11164117	ZNF514	cis	Temporal Cortex	GTEx
rs11164117	ZNF514	cis	Adipose Subcutaneous	GTEx
rs11164117	ZNF514	cis	Artery Aorta	GTEx
rs11164117	ZNF514	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95664400-95690600	Weak transcription	Right Atrium	heart
2	chr2:95664800-95686200	Enhancers	Fetal Thymus	thymus
3	chr2:95671000-95683800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:95674400-95686000	Weak transcription	Primary T cells from cord blood	blood
5	chr2:95676200-95685600	Weak transcription	Fetal Kidney	kidney
6	chr2:95677400-95681400	Enhancers	GM12878-XiMat	blood
7	chr2:95677800-95681600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:95678200-95681800	Enhancers	Brain Substantia Nigra	brain
9	chr2:95678200-95683800	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:95678600-95680800	Enhancers	Brain Angular Gyrus	brain
11	chr2:95678600-95681800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr2:95678600-95683400	Enhancers	Brain Anterior Caudate	brain
13	chr2:95679400-95680800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:95679400-95682600	Weak transcription	Thymus	Thymus
15	chr2:95679600-95681000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:95679800-95680600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:95680000-95680600	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr2:95680000-95681200	Enhancers	Fetal Stomach	stomach
19	chr2:95680200-95681200	Enhancers	Fetal Lung	lung
20	chr2:95680200-95682400	Enhancers	Fetal Muscle Trunk	muscle
21	chr2:95680200-95682600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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