Variant report

Variant	rs12343288
Chromosome Location	chr9:104308365-104308366
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	chr9:104302143..104304850-chr9:104306401..104308642,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10115763	0.89[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989553	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12342026	0.85[ASN][1000 genomes]
rs12342991	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12347518	0.89[ASN][1000 genomes]
rs13284984	0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13290720	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13295809	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs16920473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885977	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929496	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28533545	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34153995	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34727333	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004060	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739722	0.84[ASN][1000 genomes]
rs3739723	0.87[JPT][hapmap]
rs3739724	0.82[JPT][hapmap]
rs3824473	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3903804	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4119332	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs45488691	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59770438	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7030238	0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs7034754	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9299345	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv831672	chr9:104300755-104480849	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12343288	SEC61B	cis	cerebellum	SCAN
rs12343288	FOXE1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104296800-104334200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:104296800-104337400	Weak transcription	Stomach Mucosa	stomach
3	chr9:104297000-104309200	Weak transcription	HUVEC	blood vessel
4	chr9:104297000-104317600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:104297200-104309200	Weak transcription	K562	blood
6	chr9:104297600-104321200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:104297600-104330400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:104297600-104330400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:104297800-104311400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:104297800-104317400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:104297800-104318400	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr9:104297800-104320400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:104297800-104320400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:104297800-104325400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr9:104297800-104332600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:104297800-104333000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr9:104298000-104332800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr9:104298200-104311200	Strong transcription	Primary B cells from cord blood	blood
19	chr9:104298200-104328200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr9:104298200-104333200	Strong transcription	Adipose Nuclei	Adipose
21	chr9:104298400-104312800	Weak transcription	Small Intestine	intestine
22	chr9:104298400-104320000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:104298400-104333200	Strong transcription	Liver	Liver
24	chr9:104298400-104333400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr9:104298600-104325000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:104298800-104317600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr9:104299000-104333000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:104299200-104324200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:104299200-104330400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:104299400-104311400	Strong transcription	Fetal Intestine Large	intestine
31	chr9:104299600-104309200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:104299600-104311400	Strong transcription	Brain Angular Gyrus	brain
33	chr9:104299600-104321000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr9:104300000-104309000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr9:104300800-104323400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:104300800-104327000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:104301000-104314000	Weak transcription	Fetal Heart	heart
38	chr9:104301000-104320200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:104301200-104328800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr9:104301400-104323800	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr9:104301600-104333400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:104301800-104311200	Strong transcription	Fetal Kidney	kidney
43	chr9:104301800-104320400	Strong transcription	Fetal Brain Female	brain
44	chr9:104301800-104331800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:104302000-104317200	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr9:104302200-104316400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:104302200-104320800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr9:104302200-104333000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr9:104302400-104311400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr9:104302600-104317200	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links