Variant report

Variant	rs12339235
Chromosome Location	chr9:71401918-71401919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71398863..71402159-chr9:71407140..71410574,3	K562	blood:
2	chr9:71393697..71395796-chr9:71400941..71403104,3	K562	blood:
3	chr9:71400597..71404451-chr9:71406708..71409668,4	MCF-7	breast:
4	chr9:71395139..71397780-chr9:71401800..71403329,2	MCF-7	breast:
5	chr9:71401239..71403328-chr9:71403881..71406590,2	K562	blood:

Variant related genes	Relation type
ENSG00000187866	Chromatin interaction
ENSG00000236998	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10448338	0.87[CEU][hapmap]
rs10781282	0.82[CEU][hapmap]
rs10869320	0.82[CEU][hapmap]
rs10869538	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs11143691	0.88[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs11143697	0.82[EUR][1000 genomes]
rs11143715	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11143731	0.85[EUR][1000 genomes]
rs11143741	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs11143761	0.82[CEU][hapmap]
rs11143777	0.82[CEU][hapmap]
rs11143882	0.82[CEU][hapmap]
rs11143951	0.82[CEU][hapmap]
rs11144074	0.80[CEU][hapmap]
rs11144136	0.82[CEU][hapmap]
rs11144138	0.80[CEU][hapmap]
rs11144152	0.82[CEU][hapmap]
rs11144154	0.82[CEU][hapmap]
rs11144163	0.81[CEU][hapmap]
rs11144178	0.82[CEU][hapmap]
rs11144181	0.82[CEU][hapmap]
rs11144215	0.82[CEU][hapmap]
rs11144305	0.82[CEU][hapmap]
rs11144351	0.80[CEU][hapmap]
rs12340532	1.00[JPT][hapmap]
rs12341558	0.80[ASN][1000 genomes]
rs12376037	0.82[CEU][hapmap]
rs12376991	0.82[CEU][hapmap]
rs12377033	0.82[CEU][hapmap]
rs12379061	0.82[CEU][hapmap]
rs12552102	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs12555728	0.94[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1414951	0.82[CEU][hapmap]
rs1414954	0.82[CEU][hapmap]
rs17058780	0.82[CEU][hapmap]
rs17391456	0.82[CEU][hapmap]
rs17391582	0.82[CEU][hapmap]
rs17483165	0.82[CEU][hapmap]
rs4623507	0.87[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs58984094	0.94[ASN][1000 genomes]
rs62552125	0.81[EUR][1000 genomes]
rs62552126	0.80[EUR][1000 genomes]
rs62552127	0.81[EUR][1000 genomes]
rs62552128	0.81[EUR][1000 genomes]
rs62552131	0.81[EUR][1000 genomes]
rs6560361	0.82[ASN][1000 genomes]
rs7018854	0.82[CEU][hapmap]
rs7048631	0.81[ASN][1000 genomes]
rs72717924	0.81[EUR][1000 genomes]
rs73646761	0.80[ASN][1000 genomes]
rs950786	0.82[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats 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	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12339235	FAM108B1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71396000-71402400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr9:71396000-71403400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:71396000-71408200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:71396200-71409800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:71397200-71402200	Weak transcription	A549	lung
6	chr9:71397200-71403800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:71397200-71404200	Weak transcription	Esophagus	oesophagus
8	chr9:71397200-71409600	Weak transcription	Colonic Mucosa	Colon
9	chr9:71397200-71417400	Weak transcription	Lung	lung
10	chr9:71397800-71408000	Weak transcription	Gastric	stomach
11	chr9:71398600-71404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:71398600-71405400	Strong transcription	Primary B cells from cord blood	blood
13	chr9:71398800-71406000	Weak transcription	Spleen	Spleen
14	chr9:71398800-71408000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr9:71398800-71409800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:71399000-71403000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:71399000-71403000	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:71399000-71403800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr9:71399000-71404000	Weak transcription	Ovary	ovary
20	chr9:71399000-71405600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:71399000-71406200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:71399000-71408400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:71399000-71408400	Weak transcription	Stomach Mucosa	stomach
24	chr9:71399000-71420200	Weak transcription	Fetal Stomach	stomach
25	chr9:71399200-71407800	Weak transcription	GM12878-XiMat	blood
26	chr9:71399400-71404800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:71399600-71403000	Weak transcription	HepG2	liver
28	chr9:71399600-71407200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:71399800-71413200	Weak transcription	Dnd41	blood
30	chr9:71400000-71403000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:71400200-71403000	Weak transcription	Fetal Intestine Large	intestine
32	chr9:71400200-71403000	Weak transcription	Psoas Muscle	Psoas
33	chr9:71400200-71403200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr9:71400200-71405800	Weak transcription	Brain Angular Gyrus	brain
35	chr9:71400200-71406000	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:71400400-71402800	Weak transcription	Thymus	Thymus
37	chr9:71400400-71403600	Weak transcription	Right Ventricle	heart
38	chr9:71400400-71404600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr9:71400400-71408000	Weak transcription	K562	blood
40	chr9:71400400-71408600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:71400600-71402000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:71400600-71409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:71400800-71402000	Weak transcription	Pancreas	Pancrea
44	chr9:71400800-71402600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr9:71400800-71402800	Weak transcription	Fetal Heart	heart
46	chr9:71400800-71403000	Weak transcription	Left Ventricle	heart
47	chr9:71400800-71403600	Weak transcription	Brain Hippocampus Middle	brain
48	chr9:71400800-71403800	Weak transcription	Right Atrium	heart
49	chr9:71400800-71409000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr9:71400800-71409000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links