Variant report

Variant	rs12004862
Chromosome Location	chr9:3513729-3513730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:3440838..3441394-chr9:3513388..3514228,2	MCF-7	breast:
2	chr9:3512475..3514948-chr9:3515392..3517611,2	MCF-7	breast:
3	chr9:3505863..3515695-chr9:3520675..3529318,33	K562	blood:
4	chr9:3331504..3332243-chr9:3512940..3513736,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232104	Chromatin interaction
ENSG00000080298	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10114162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs10114838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10115088	0.87[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs10115578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs10119982	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap]
rs10121096	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs10758299	0.87[EUR][1000 genomes]
rs10814188	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10814189	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10814190	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10814208	0.87[CEU][hapmap];0.95[JPT][hapmap]
rs10814233	0.87[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs10972359	0.81[EUR][1000 genomes]
rs10972435	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs10972438	0.83[EUR][1000 genomes]
rs1133467	0.83[EUR][1000 genomes]
rs12238307	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs12340274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs12345145	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12353393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12553270	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs1342542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2027089	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs28510559	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3954945	0.83[EUR][1000 genomes]
rs7022948	0.87[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs7026025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7027862	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs7041399	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7857554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7861625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7864107	0.83[EUR][1000 genomes]
rs7871777	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs881167	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs9792451	0.83[EUR][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	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
2	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3474400-3524400	Weak transcription	Thymus	Thymus
2	chr9:3480600-3524600	Weak transcription	Left Ventricle	heart
3	chr9:3500400-3516800	Weak transcription	Psoas Muscle	Psoas
4	chr9:3503000-3524400	Weak transcription	Fetal Thymus	thymus
5	chr9:3506800-3522000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr9:3509000-3516600	Weak transcription	HSMMtube	muscle
7	chr9:3509000-3516800	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:3509000-3523800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:3509000-3523800	Weak transcription	HSMM	muscle
10	chr9:3509000-3524400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:3509200-3522000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr9:3509400-3516800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:3509400-3517800	Weak transcription	Primary T cells from cord blood	blood
14	chr9:3509400-3522800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:3509400-3523600	Weak transcription	Primary B cells from cord blood	blood
16	chr9:3509600-3516800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:3510000-3516800	Weak transcription	Brain Anterior Caudate	brain
18	chr9:3510200-3516800	Weak transcription	Brain Germinal Matrix	brain
19	chr9:3510200-3521800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr9:3510400-3513800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:3510400-3520600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr9:3510400-3521600	Weak transcription	Dnd41	blood
23	chr9:3510600-3520400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:3511000-3513800	ZNF genes & repeats	GM12878-XiMat	blood
25	chr9:3511800-3515600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr9:3511800-3522000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:3511800-3522200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:3511800-3523600	Weak transcription	Fetal Lung	lung
29	chr9:3512000-3516200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:3512000-3516800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:3512000-3520600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr9:3512000-3524200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:3512000-3524400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:3512000-3525000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr9:3512200-3516800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:3512200-3520400	Weak transcription	HepG2	liver
37	chr9:3512200-3522000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:3512200-3523200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:3512600-3515600	Enhancers	A549	lung
40	chr9:3513000-3514000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr9:3513000-3514400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr9:3513200-3514000	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr9:3513400-3513800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr9:3513400-3513800	Enhancers	K562	blood
45	chr9:3513400-3514200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr9:3513400-3514400	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr9:3513600-3513800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr9:3513600-3513800	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links