Variant report

Variant	rs10115578
Chromosome Location	chr9:3484373-3484374
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	chr9:3481303..3484512-chr9:3524609..3529415,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000080298	Chromatin interaction
ENSG00000232104	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10113926	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10114162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115088	0.87[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs10117292	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10119475	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119982	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121096	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123122	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10123592	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10124613	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10758273	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758286	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10814148	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10814189	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10814190	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10814208	0.87[CEU][hapmap];0.95[JPT][hapmap]
rs10814233	0.87[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs10972184	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10972200	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10972435	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs12004862	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]
rs12238307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340274	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]
rs12353393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12553270	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs1342542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2027089	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7022948	0.87[CEU][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap]
rs7026025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027858	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7027862	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs7037463	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7041399	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7857554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7861625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871777	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs881167	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	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
9	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10115578	PPTC7	trans	brain	seeQTL
rs10115578	PEX5L	trans	brain	seeQTL
rs10115578	TAOK1	trans	brain	seeQTL
rs10115578	NRIP3	trans	brain	seeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3468600-3484800	Weak transcription	Ovary	ovary
2	chr9:3468800-3496600	Weak transcription	HSMMtube	muscle
3	chr9:3469400-3495600	Weak transcription	Fetal Kidney	kidney
4	chr9:3473600-3496600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:3474000-3493600	Weak transcription	Fetal Stomach	stomach
6	chr9:3474400-3490800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:3474400-3524400	Weak transcription	Thymus	Thymus
8	chr9:3474600-3486000	Weak transcription	Small Intestine	intestine
9	chr9:3475000-3492600	Weak transcription	Lung	lung
10	chr9:3475800-3485600	Weak transcription	Spleen	Spleen
11	chr9:3477400-3485400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:3477600-3484400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:3477600-3487000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr9:3477600-3495600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:3477800-3486200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:3478000-3486000	Weak transcription	Liver	Liver
17	chr9:3478200-3484400	Weak transcription	Brain Anterior Caudate	brain
18	chr9:3478200-3485200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:3478200-3488000	Weak transcription	Fetal Intestine Large	intestine
20	chr9:3478800-3485800	Weak transcription	Fetal Brain Female	brain
21	chr9:3478800-3485800	Weak transcription	Dnd41	blood
22	chr9:3479000-3486200	Weak transcription	HepG2	liver
23	chr9:3479000-3498800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:3479200-3491200	Weak transcription	Adipose Nuclei	Adipose
25	chr9:3479200-3500200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:3479200-3507200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:3479400-3496400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:3479400-3508000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:3479800-3492200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:3479800-3508800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr9:3479800-3511600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:3480000-3506400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr9:3480200-3486400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:3480200-3490200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:3480200-3499800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr9:3480400-3486400	Weak transcription	Aorta	Aorta
37	chr9:3480400-3489800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr9:3480400-3496400	Weak transcription	NH-A	brain
39	chr9:3480400-3508000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr9:3480600-3485600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:3480600-3491800	Weak transcription	Fetal Intestine Small	intestine
42	chr9:3480600-3495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:3480600-3500200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr9:3480600-3508800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr9:3480600-3510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:3480600-3524600	Weak transcription	Left Ventricle	heart
47	chr9:3480800-3486200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:3480800-3489400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:3480800-3491400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:3480800-3507400	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links