Variant report

Variant	rs12686258
Chromosome Location	chr9:101534397-101534398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101527672..101531137-chr9:101531732..101534659,4	K562	blood:
2	chr9:101529536..101531774-chr9:101533409..101535108,2	K562	blood:
3	chr9:101534213..101537484-chr9:101539835..101542863,3	MCF-7	breast:
4	chr9:101525437..101530205-chr9:101533876..101536936,4	MCF-7	breast:
5	chr9:101523511..101525815-chr9:101533805..101535454,2	MCF-7	breast:

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10987602	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10987748	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2295924	0.88[CHD][hapmap];0.89[JPT][hapmap]
rs7043234	0.89[JPT][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	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12686258	INVS	cis	cerebellum	SCAN
rs12686258	FBP2	cis	cerebellum	SCAN
rs12686258	FANCC	cis	parietal	SCAN
rs12686258	ZNF189	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101494000-101535200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr9:101494400-101553000	Weak transcription	Fetal Heart	heart
3	chr9:101496600-101549400	Weak transcription	Small Intestine	intestine
4	chr9:101503000-101537400	Weak transcription	HUVEC	blood vessel
5	chr9:101506800-101553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr9:101508600-101557400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:101510000-101534600	Weak transcription	NHLF	lung
8	chr9:101514400-101553400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:101517600-101537400	Weak transcription	NH-A	brain
10	chr9:101518200-101537400	Weak transcription	Hela-S3	cervix
11	chr9:101518800-101557200	Weak transcription	Psoas Muscle	Psoas
12	chr9:101521200-101557600	Weak transcription	Fetal Brain Male	brain
13	chr9:101521600-101537000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:101523600-101542600	Weak transcription	Stomach Mucosa	stomach
15	chr9:101525800-101537000	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:101526400-101536600	Strong transcription	A549	lung
17	chr9:101526400-101538200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:101526400-101549400	Strong transcription	Stomach Smooth Muscle	stomach
19	chr9:101526600-101536000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr9:101526800-101536800	Strong transcription	Adipose Nuclei	Adipose
21	chr9:101526800-101537200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:101527200-101536800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:101527400-101536800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:101527400-101536800	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:101527400-101536800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:101527400-101537400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:101527400-101537600	Strong transcription	Primary T cells from cord blood	blood
28	chr9:101527600-101536800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:101527600-101537000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr9:101527600-101537400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr9:101527800-101536800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:101527800-101537600	Strong transcription	Fetal Muscle Leg	muscle
33	chr9:101527800-101538000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:101528000-101536800	Strong transcription	Ovary	ovary
35	chr9:101528200-101534800	Weak transcription	HepG2	liver
36	chr9:101528200-101543800	Weak transcription	HMEC	breast
37	chr9:101528800-101536600	Strong transcription	Brain Hippocampus Middle	brain
38	chr9:101528800-101537000	Strong transcription	Rectal Smooth Muscle	rectum
39	chr9:101528800-101537800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:101529000-101536200	Strong transcription	HSMM	muscle
41	chr9:101529000-101536800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:101529000-101536800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr9:101529000-101537000	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr9:101529000-101537800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr9:101529200-101536400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:101529200-101536800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr9:101529200-101537000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:101529200-101537400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:101529400-101536000	Strong transcription	Brain Substantia Nigra	brain
50	chr9:101529400-101536400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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