Variant report

Variant	rs12340274
Chromosome Location	chr9:3500471-3500472
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:3500140..3503117-chr9:3505256..3509401,4	K562	blood:
2	chr9:3478739..3481374-chr9:3498869..3500820,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10113926	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10114162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10114838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10115088	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs10115578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10117292	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119475	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119982	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10121096	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10123122	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10123592	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10124613	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10758273	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758286	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10814148	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10814189	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10814190	0.83[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs10814208	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs10814233	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs10972183	0.80[AMR][1000 genomes]
rs10972184	0.85[EUR][1000 genomes]
rs10972200	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10972435	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs12004862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs12238307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12353393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12553270	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs1342542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2027089	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs7022948	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7026025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7027858	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7027862	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7037463	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7041399	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7857554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7871777	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs881167	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1019324	chr9:3436845-3502815	ZNF genes & repeats Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	nsv892091	chr9:3459635-3508284	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv539944	chr9:3476471-3535344	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
11	nsv522711	chr9:3480671-3500471	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3474400-3524400	Weak transcription	Thymus	Thymus
2	chr9:3479200-3507200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:3479400-3508000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:3479800-3508800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:3479800-3511600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:3480000-3506400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:3480400-3508000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:3480600-3508800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:3480600-3510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:3480600-3524600	Weak transcription	Left Ventricle	heart
11	chr9:3480800-3507400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:3483200-3508400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:3484800-3504200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:3484800-3507200	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:3485000-3507400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr9:3485200-3507800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:3490000-3508000	Weak transcription	Primary B cells from cord blood	blood
18	chr9:3494000-3501000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:3494400-3501200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr9:3498400-3500800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:3498600-3503000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:3498800-3500800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr9:3498800-3508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:3499000-3508600	Weak transcription	HSMM	muscle
25	chr9:3499200-3501000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:3499200-3508800	Weak transcription	HSMMtube	muscle
27	chr9:3499600-3501000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:3499800-3500800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr9:3500000-3508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:3500200-3501000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr9:3500200-3502600	Weak transcription	NH-A	brain
32	chr9:3500200-3505800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr9:3500200-3508800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:3500400-3502600	Weak transcription	GM12878-XiMat	blood
35	chr9:3500400-3502800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr9:3500400-3502800	Weak transcription	Osteobl	bone
37	chr9:3500400-3505600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:3500400-3505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:3500400-3505800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr9:3500400-3507200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:3500400-3507400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:3500400-3507800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:3500400-3507800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:3500400-3507800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr9:3500400-3508400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr9:3500400-3508600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr9:3500400-3516800	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links