Variant report

Variant	rs4485423
Chromosome Location	chr17:16930985-16930986
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16930112..16931615-chr17:16942008..16944719,2	K562	blood:
2	chr17:16924719..16926363-chr17:16928237..16932446,3	MCF-7	breast:
3	chr17:16923260..16925095-chr17:16929732..16931336,2	MCF-7	breast:
4	chr17:16904092..16907044-chr17:16930901..16933093,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4452010	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs4985779	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4985782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72637385	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72637386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[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	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv907727	chr17:16892265-16938582	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv543231	chr17:16926227-16950644	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4485423	TOM1L2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16925200-16931000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr17:16925400-16931000	Enhancers	A549	lung
3	chr17:16925600-16931800	Weak transcription	Osteobl	bone
4	chr17:16926000-16931400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:16926600-16931400	Weak transcription	Brain Angular Gyrus	brain
6	chr17:16926600-16931400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr17:16926800-16931200	Weak transcription	Brain Substantia Nigra	brain
8	chr17:16928600-16931800	Weak transcription	Adipose Nuclei	Adipose
9	chr17:16928600-16933800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr17:16928800-16934000	Enhancers	Fetal Intestine Large	intestine
11	chr17:16929000-16931400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:16929000-16931400	Weak transcription	Right Ventricle	heart
13	chr17:16929000-16931400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr17:16929000-16931600	Weak transcription	Right Atrium	heart
15	chr17:16929200-16931600	Weak transcription	Left Ventricle	heart
16	chr17:16929400-16931000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:16929400-16931400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:16929400-16931400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr17:16929400-16932000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr17:16929400-16932200	Weak transcription	Fetal Thymus	thymus
21	chr17:16929600-16931000	Weak transcription	Fetal Heart	heart
22	chr17:16929600-16931600	Weak transcription	Fetal Kidney	kidney
23	chr17:16929800-16931600	Weak transcription	Fetal Lung	lung
24	chr17:16930200-16931600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:16930200-16936200	Enhancers	Fetal Muscle Leg	muscle
26	chr17:16930400-16934000	Enhancers	Fetal Intestine Small	intestine
27	chr17:16930400-16934000	Enhancers	Stomach Mucosa	stomach
28	chr17:16930400-16934400	Enhancers	Placenta	Placenta
29	chr17:16930400-16936600	Enhancers	Fetal Muscle Trunk	muscle
30	chr17:16930600-16931200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr17:16930600-16931400	Flanking Active TSS	Hela-S3	cervix
32	chr17:16930600-16931400	Enhancers	NHEK	skin
33	chr17:16930600-16931600	Enhancers	Esophagus	oesophagus
34	chr17:16930600-16931800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr17:16930600-16933000	Enhancers	Gastric	stomach
36	chr17:16930600-16933200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:16930600-16933600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr17:16930600-16934400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:16930600-16936000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr17:16930600-16936200	Enhancers	HMEC	breast
41	chr17:16930600-16937600	Enhancers	HSMMtube	muscle
42	chr17:16930800-16931000	Enhancers	Brain Anterior Caudate	brain
43	chr17:16930800-16931200	Enhancers	K562	blood
44	chr17:16930800-16931600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr17:16930800-16931600	Enhancers	HSMM	muscle
46	chr17:16930800-16931800	Enhancers	Brain Cingulate Gyrus	brain
47	chr17:16930800-16931800	Enhancers	Colonic Mucosa	Colon
48	chr17:16930800-16932000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:16930800-16932000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:16930800-16932200	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links