Variant report

Variant	rs9969804
Chromosome Location	chr9:95429120-95429121
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95416446..95420766-chr9:95422078..95429343,12	MCF-7	breast:
2	chr9:95404607..95407268-chr9:95427098..95429531,2	MCF-7	breast:
3	chr9:95428577..95430199-chr9:95472529..95474207,2	MCF-7	breast:
4	chr9:95429103..95431144-chr9:95506974..95509653,2	MCF-7	breast:
5	chr9:95428069..95433526-chr9:95524054..95531235,7	MCF-7	breast:
6	chr9:95055089..95057841-chr9:95428925..95431600,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction
ENSG00000196305	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10115937	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10117377	0.82[EUR][1000 genomes]
rs10120210	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10120292	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10121218	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1015791	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10435919	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10739929	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10761167	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10761168	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10761169	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10761170	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821013	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10992415	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10992439	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1111047	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12554627	0.89[ASW][hapmap]
rs1536423	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs2007245	0.83[AMR][1000 genomes]
rs2018717	0.81[MEX][hapmap];0.81[TSI][hapmap]
rs2131918	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2296668	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes]
rs4266708	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4744142	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6479424	0.92[CEU][hapmap];0.93[GIH][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6479427	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479429	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7021624	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7043114	0.96[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7862310	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7863755	0.82[AMR][1000 genomes]
rs7864757	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7873646	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7875225	0.81[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs912260	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs912262	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9886781	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant related diseases (count:1)

Disease	PMID	Source
Height	20881960	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9969804	ZNF484	cis	parietal	SCAN
rs9969804	IPPK	cis	cerebellum	SCAN
rs9969804	CENPP	cis	parietal	SCAN
rs9969804	CENPP	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95409800-95431000	Weak transcription	Fetal Kidney	kidney
2	chr9:95411000-95431400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:95412000-95431000	Weak transcription	Fetal Brain Male	brain
4	chr9:95412400-95431200	Weak transcription	Small Intestine	intestine
5	chr9:95417800-95431000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:95418000-95431000	Weak transcription	Psoas Muscle	Psoas
7	chr9:95418600-95431000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:95420800-95430800	Weak transcription	HSMMtube	muscle
9	chr9:95420800-95431000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:95420800-95431000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:95421200-95430800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:95421200-95430800	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:95421200-95431000	Weak transcription	Colonic Mucosa	Colon
14	chr9:95422200-95429800	Strong transcription	Fetal Intestine Small	intestine
15	chr9:95422400-95431200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:95422800-95430800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:95422800-95431000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:95422800-95431400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:95423400-95429800	Strong transcription	Fetal Stomach	stomach
20	chr9:95424000-95429800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr9:95424200-95430600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr9:95425200-95430000	Strong transcription	Fetal Muscle Leg	muscle
23	chr9:95426200-95431000	Weak transcription	Primary B cells from cord blood	blood
24	chr9:95426600-95429200	Weak transcription	Hela-S3	cervix
25	chr9:95426600-95429400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr9:95426600-95430800	Weak transcription	HepG2	liver
27	chr9:95427200-95429800	Genic enhancers	NHEK	skin
28	chr9:95427200-95431000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:95427400-95429800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:95427400-95429800	Enhancers	Liver	Liver
31	chr9:95427400-95430800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:95427400-95431000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:95427400-95431000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:95427600-95429800	Strong transcription	HSMM	muscle
35	chr9:95427600-95430600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr9:95427600-95430600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr9:95427600-95430800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:95427600-95430800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:95427600-95430800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr9:95427600-95431000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:95427600-95431000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr9:95427600-95431000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr9:95427800-95429800	Genic enhancers	GM12878-XiMat	blood
44	chr9:95427800-95430800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr9:95427800-95431000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:95428000-95429800	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr9:95428000-95429800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr9:95428000-95430200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:95428000-95431200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:95428200-95429200	Genic enhancers	Fetal Brain Female	brain

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