Variant report

Variant	rs321654
Chromosome Location	chr18:8625642-8625643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:8608973..8610976-chr18:8624181..8625797,2	MCF-7	breast:
2	chr18:8625509..8627110-chr18:8627947..8629473,2	MCF-7	breast:
3	chr18:8625177..8627727-chr18:8631333..8633538,2	K562	blood:
4	chr18:8624127..8626871-chr18:8632605..8635098,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206418	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11876907	0.85[MEX][hapmap]
rs1250161	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs321653	0.81[AFR][1000 genomes]
rs321657	0.92[YRI][hapmap]
rs321663	1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap]
rs321664	0.84[ASW][hapmap];0.92[YRI][hapmap]
rs321667	0.83[ASW][hapmap];0.92[YRI][hapmap]
rs399600	1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes]
rs55906430	0.87[ASN][1000 genomes]
rs7237512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs72936887	0.91[ASN][1000 genomes]
rs72938803	0.82[ASN][1000 genomes]
rs9965007	0.89[ASW][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458018	chr18:8110805-8645907	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv576426	chr18:8110805-8645907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv2200	chr18:8618182-8663130	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs321654	Contig36728_RC	cis	multi-tissue	Pritchard
rs321654	RAB12	cis	Liver	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8610600-8634400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:8616600-8634600	Weak transcription	NH-A	brain
3	chr18:8621000-8631200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr18:8621600-8633400	Weak transcription	Fetal Brain Male	brain
5	chr18:8621800-8633000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr18:8623400-8627800	Enhancers	Fetal Heart	heart
7	chr18:8623400-8630800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
8	chr18:8623600-8626200	Weak transcription	Fetal Kidney	kidney
9	chr18:8623600-8627000	Strong transcription	K562	blood
10	chr18:8623600-8640600	Strong transcription	Dnd41	blood
11	chr18:8623800-8625800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr18:8623800-8627200	Strong transcription	Primary T cells from cord blood	blood
13	chr18:8624000-8626000	Weak transcription	HSMMtube	muscle
14	chr18:8624200-8625800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr18:8624200-8625800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr18:8624200-8625800	Weak transcription	Colonic Mucosa	Colon
17	chr18:8624200-8626200	Enhancers	Brain Substantia Nigra	brain
18	chr18:8624200-8626600	Weak transcription	NHLF	lung
19	chr18:8624200-8629400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr18:8624200-8629600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr18:8624200-8631000	Weak transcription	Right Atrium	heart
22	chr18:8624200-8632000	Weak transcription	Right Ventricle	heart
23	chr18:8624200-8633400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr18:8624200-8633400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr18:8624200-8633600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr18:8624200-8638200	Weak transcription	Stomach Mucosa	stomach
27	chr18:8624200-8641200	Weak transcription	Small Intestine	intestine
28	chr18:8624400-8626000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
29	chr18:8624400-8626600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr18:8624400-8627800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr18:8624600-8626800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr18:8624600-8627400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr18:8624600-8627800	Strong transcription	HMEC	breast
34	chr18:8624600-8628000	Strong transcription	Primary B cells from cord blood	blood
35	chr18:8624600-8628400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr18:8624600-8630800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
37	chr18:8624600-8631000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr18:8624600-8640200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr18:8624600-8640400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr18:8624600-8640800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:8624800-8626400	Strong transcription	A549	lung
42	chr18:8624800-8627000	Genic enhancers	HepG2	liver
43	chr18:8624800-8627600	Strong transcription	NHDF-Ad	bronchial
44	chr18:8624800-8627800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr18:8624800-8628000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:8624800-8628400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr18:8624800-8628600	Enhancers	Brain Angular Gyrus	brain
48	chr18:8624800-8641600	Strong transcription	GM12878-XiMat	blood
49	chr18:8625000-8626000	Genic enhancers	H1 Cell Line	embryonic stem cell
50	chr18:8625000-8627000	Strong transcription	HSMM	muscle

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