Variant report

Variant	rs7859380
Chromosome Location	chr9:95616149-95616150
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	chr9:95614113..95616459-chr9:95617229..95618741,2	K562	blood:
2	chr9:95614976..95617847-chr9:95627258..95628901,2	K562	blood:

Variant related genes	Relation type
ENSG00000127081	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10115872	0.81[EUR][1000 genomes]
rs10123843	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs10123870	0.81[EUR][1000 genomes]
rs1022834	0.89[ASN][1000 genomes]
rs1047868	0.96[ASN][1000 genomes]
rs10739933	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs10739934	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs10761173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10821020	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10821023	0.96[ASN][1000 genomes]
rs10821027	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821030	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10821031	0.82[EUR][1000 genomes]
rs10821035	0.81[EUR][1000 genomes]
rs10992484	0.96[ASN][1000 genomes]
rs10992489	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs12337654	0.81[CEU][hapmap]
rs12338961	0.82[EUR][1000 genomes]
rs13295605	0.90[ASN][1000 genomes]
rs1810685	0.96[ASN][1000 genomes]
rs1810686	0.94[ASN][1000 genomes]
rs1810687	0.96[ASN][1000 genomes]
rs1972214	0.96[ASN][1000 genomes]
rs1998483	0.96[ASN][1000 genomes]
rs2009444	0.96[ASN][1000 genomes]
rs2146718	0.86[EUR][1000 genomes]
rs4625094	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744148	0.96[ASN][1000 genomes]
rs4744150	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs6479434	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7032277	0.81[EUR][1000 genomes]
rs7039812	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs7040645	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7049211	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7847713	0.82[EUR][1000 genomes]
rs7850036	0.96[ASN][1000 genomes]
rs7865255	0.96[ASN][1000 genomes]
rs7866339	0.94[ASN][1000 genomes]
rs7868123	0.96[ASN][1000 genomes]
rs7869498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7873021	0.82[EUR][1000 genomes]
rs7873259	0.92[ASN][1000 genomes]
rs7873819	0.96[ASN][1000 genomes]
rs7873954	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9775485	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv893574	chr9:95580376-95688099	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7859380	FANCC	cis	cerebellum	SCAN
rs7859380	ZNF484	cis	cerebellum	SCAN
rs7859380	ZNF484	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95598000-95616800	ZNF genes & repeats	Liver	Liver
2	chr9:95603400-95616200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:95605000-95624200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:95606800-95619600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:95607600-95616200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr9:95608200-95616200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:95608200-95616200	ZNF genes & repeats	GM12878-XiMat	blood
8	chr9:95609000-95616400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:95609000-95639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:95610800-95617600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:95610800-95619800	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr9:95611000-95618600	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:95611000-95619800	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr9:95611000-95620000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:95611000-95620000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr9:95611200-95620600	Strong transcription	Left Ventricle	heart
17	chr9:95611200-95632800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:95611600-95619800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:95611600-95620000	Strong transcription	Osteobl	bone
20	chr9:95612200-95616400	Strong transcription	Gastric	stomach
21	chr9:95612400-95617200	Strong transcription	Fetal Stomach	stomach
22	chr9:95612400-95618400	Strong transcription	HSMMtube	muscle
23	chr9:95612400-95618600	Strong transcription	Brain Germinal Matrix	brain
24	chr9:95612400-95618800	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr9:95612400-95622000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr9:95612400-95622200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:95612400-95624200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:95612600-95620200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:95612600-95620400	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr9:95612600-95620400	Strong transcription	Fetal Muscle Leg	muscle
31	chr9:95612800-95618600	Strong transcription	Adipose Nuclei	Adipose
32	chr9:95613200-95617600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:95613200-95620400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:95613400-95619600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:95613400-95619800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:95613400-95620000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr9:95613400-95621600	Weak transcription	HMEC	breast
38	chr9:95613600-95617600	Weak transcription	NHEK	skin
39	chr9:95613600-95617800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:95613800-95618400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr9:95613800-95618800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:95614000-95617600	Strong transcription	Primary B cells from cord blood	blood
43	chr9:95614000-95624200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr9:95614200-95618600	Strong transcription	Rectal Smooth Muscle	rectum
45	chr9:95614200-95620400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:95614400-95616800	Strong transcription	Fetal Intestine Small	intestine
47	chr9:95614400-95618200	Strong transcription	Stomach Smooth Muscle	stomach
48	chr9:95614400-95620400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr9:95614800-95618400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr9:95615000-95616200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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