Variant report

Variant	rs12552102
Chromosome Location	chr9:71403821-71403822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71392687..71396802-chr9:71403243..71407898,5	MCF-7	breast:
2	chr9:71400597..71404451-chr9:71406708..71409668,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187866	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10448338	0.93[CEU][hapmap]
rs10781282	0.86[CEU][hapmap]
rs10869320	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs11143608	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143691	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143697	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143715	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs11143731	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143741	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143761	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs11143777	0.86[CEU][hapmap]
rs11143882	0.86[CEU][hapmap]
rs11143900	0.80[CEU][hapmap]
rs11143951	0.86[CEU][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap]
rs11144027	1.00[ASN][1000 genomes]
rs11144059	0.86[CEU][hapmap]
rs11144074	0.85[CEU][hapmap]
rs11144136	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs11144138	0.86[CEU][hapmap]
rs11144152	0.86[CEU][hapmap]
rs11144154	0.86[CEU][hapmap]
rs11144163	0.85[CEU][hapmap]
rs11144178	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs11144181	0.86[CEU][hapmap]
rs11144206	0.82[MEX][hapmap]
rs11144215	0.86[CEU][hapmap]
rs11144305	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs11144351	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs12000088	1.00[ASN][1000 genomes]
rs12339235	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs12376037	0.86[CEU][hapmap]
rs12376991	0.86[CEU][hapmap]
rs12377033	0.86[CEU][hapmap]
rs12379061	0.86[CEU][hapmap]
rs12380573	0.82[MEX][hapmap]
rs12555728	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412987	1.00[ASN][1000 genomes]
rs1414951	0.86[CEU][hapmap]
rs1414954	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs17058780	0.86[CEU][hapmap]
rs17058792	0.80[CEU][hapmap]
rs17391456	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs17391582	0.86[CEU][hapmap]
rs17483165	0.86[CEU][hapmap]
rs4623507	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552125	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552126	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552127	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552128	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552130	1.00[ASN][1000 genomes]
rs62552131	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865397	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs950786	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs12552102	FAM108B1	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71396000-71408200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:71396200-71409800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:71397200-71404200	Weak transcription	Esophagus	oesophagus
4	chr9:71397200-71409600	Weak transcription	Colonic Mucosa	Colon
5	chr9:71397200-71417400	Weak transcription	Lung	lung
6	chr9:71397800-71408000	Weak transcription	Gastric	stomach
7	chr9:71398600-71404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:71398600-71405400	Strong transcription	Primary B cells from cord blood	blood
9	chr9:71398800-71406000	Weak transcription	Spleen	Spleen
10	chr9:71398800-71408000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:71398800-71409800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:71399000-71404000	Weak transcription	Ovary	ovary
13	chr9:71399000-71405600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:71399000-71406200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:71399000-71408400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:71399000-71408400	Weak transcription	Stomach Mucosa	stomach
17	chr9:71399000-71420200	Weak transcription	Fetal Stomach	stomach
18	chr9:71399200-71407800	Weak transcription	GM12878-XiMat	blood
19	chr9:71399400-71404800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:71399600-71407200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:71399800-71413200	Weak transcription	Dnd41	blood
22	chr9:71400200-71405800	Weak transcription	Brain Angular Gyrus	brain
23	chr9:71400200-71406000	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:71400400-71404600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:71400400-71408000	Weak transcription	K562	blood
26	chr9:71400400-71408600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:71400600-71409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:71400800-71409000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:71400800-71409000	Weak transcription	Adipose Nuclei	Adipose
30	chr9:71400800-71409000	Weak transcription	Small Intestine	intestine
31	chr9:71401000-71404600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr9:71401000-71404800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:71401000-71407000	Weak transcription	Brain Germinal Matrix	brain
34	chr9:71401600-71405000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr9:71401800-71404400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr9:71401800-71404600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:71401800-71404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:71401800-71405000	Strong transcription	Fetal Intestine Small	intestine
39	chr9:71402000-71405400	Weak transcription	Aorta	Aorta
40	chr9:71402400-71404200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr9:71402400-71405600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:71402600-71405800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr9:71402600-71413400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr9:71402600-71413600	Weak transcription	Primary T cells from cord blood	blood
45	chr9:71402800-71404200	Enhancers	Fetal Heart	heart
46	chr9:71403000-71404200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr9:71403000-71404600	Strong transcription	HepG2	liver
48	chr9:71403000-71404800	Strong transcription	Fetal Intestine Large	intestine
49	chr9:71403000-71405600	Enhancers	Left Ventricle	heart
50	chr9:71403200-71405000	Weak transcription	Primary monocytes fromperipheralblood	blood

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