Variant report

Variant	rs7866848
Chromosome Location	chr9:97505608-97505609
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	chr9:97494025..97495913-chr9:97503226..97505755,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1016013	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10821401	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10993365	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10993372	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10993377	0.85[EUR][1000 genomes]
rs10993398	0.92[CEU][hapmap];0.95[YRI][hapmap]
rs12235316	0.92[CEU][hapmap]
rs1751434	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs183066	1.00[CEU][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2183958	0.81[EUR][1000 genomes]
rs2584806	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28540393	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35487382	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs356131	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356141	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs368138	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs391784	0.96[CEU][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs406654	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs414253	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4385527	0.96[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs446540	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4744369	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4744378	0.96[CEU][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4744403	0.96[CEU][hapmap]
rs4744411	0.92[CEU][hapmap]
rs7019720	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7026071	0.85[EUR][1000 genomes]
rs7851726	1.00[CEU][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7853195	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041922	chr9:97444976-97536753	Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2764145	chr9:97495261-97505608	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7866848	CNN3	trans	lymphoblastoid	seeQTL
rs7866848	FANCC	cis	lymphoblastoid	seeQTL
rs7866848	GPER	trans	lymphoblastoid	seeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97489600-97506000	Weak transcription	Lung	lung
2	chr9:97489600-97524800	Weak transcription	Esophagus	oesophagus
3	chr9:97489800-97505800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:97489800-97505800	Weak transcription	Right Ventricle	heart
5	chr9:97489800-97508000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr9:97489800-97511000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:97489800-97511400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:97489800-97511600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:97489800-97521600	Weak transcription	Fetal Thymus	thymus
10	chr9:97489800-97522000	Weak transcription	Thymus	Thymus
11	chr9:97489800-97522400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:97490000-97510600	Weak transcription	Primary T cells from cord blood	blood
13	chr9:97490000-97510800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:97490000-97510800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:97490000-97510800	Weak transcription	Fetal Brain Female	brain
16	chr9:97490000-97510800	Weak transcription	NHDF-Ad	bronchial
17	chr9:97490000-97511600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:97490000-97511600	Weak transcription	Osteobl	bone
19	chr9:97490000-97512200	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:97490000-97519400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:97490000-97521600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:97490200-97508800	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:97490200-97510800	Weak transcription	GM12878-XiMat	blood
24	chr9:97490200-97511000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:97490200-97511000	Weak transcription	NHEK	skin
26	chr9:97490200-97512200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:97490200-97519200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:97490400-97508800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:97490400-97508800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:97490400-97511400	Weak transcription	Hela-S3	cervix
31	chr9:97490400-97511600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr9:97490600-97510800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:97491000-97511000	Weak transcription	Dnd41	blood
34	chr9:97491400-97507800	Weak transcription	Brain Germinal Matrix	brain
35	chr9:97496400-97511000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:97496800-97511600	Weak transcription	Left Ventricle	heart
37	chr9:97497000-97510000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:97497000-97510800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:97497000-97511400	Weak transcription	Adipose Nuclei	Adipose
40	chr9:97497000-97511600	Weak transcription	Psoas Muscle	Psoas
41	chr9:97497000-97522000	Weak transcription	Placenta	Placenta
42	chr9:97497200-97522200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:97497600-97511400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:97499200-97505800	Weak transcription	Gastric	stomach
45	chr9:97499400-97508800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr9:97499400-97511600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:97499600-97508000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:97500200-97508400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:97502800-97518800	Weak transcription	K562	blood
50	chr9:97503000-97509200	Weak transcription	Brain Anterior Caudate	brain

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