Variant report

Variant	rs331377
Chromosome Location	chr9:95243549-95243550
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	chr9:95238987..95240540-chr9:95243033..95244624,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10761156	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs1152759	0.93[CEU][hapmap]
rs1175788	0.92[CEU][hapmap]
rs1923599	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2025389	0.93[CEU][hapmap];0.81[TSI][hapmap]
rs2031262	0.93[CEU][hapmap];0.81[TSI][hapmap]
rs2147060	0.89[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap]
rs230222	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs3174352	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs331379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs331380	0.93[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs331381	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736835	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs710163	0.89[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7867300	0.89[ASW][hapmap];0.93[CEU][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9409664	0.89[CEU][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1049599	chr9:95170139-95265558	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs331377	SUSD3	cis	multi-tissue	Pritchard
rs331377	FANCC	cis	cerebellum	SCAN
rs331377	ZNF484	cis	cerebellum	SCAN
rs331377	CENPP	cis	parietal	SCAN
rs331377	ZNF484	cis	parietal	SCAN
rs331377	CENPP	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95231800-95268800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:95235400-95251600	Weak transcription	Psoas Muscle	Psoas
3	chr9:95241200-95243600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:95241200-95243600	Enhancers	Stomach Mucosa	stomach
5	chr9:95241200-95244000	Enhancers	Fetal Heart	heart
6	chr9:95241200-95246800	Enhancers	Fetal Lung	lung
7	chr9:95241400-95251800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:95241400-95255000	Weak transcription	Esophagus	oesophagus
9	chr9:95241600-95243800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr9:95241600-95245600	Weak transcription	Lung	lung
11	chr9:95241800-95243600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr9:95241800-95243800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:95241800-95244800	Active TSS	Fetal Muscle Leg	muscle
14	chr9:95241800-95245200	Weak transcription	Ovary	ovary
15	chr9:95242000-95243800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:95242000-95243800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr9:95242000-95244000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr9:95242000-95244800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr9:95242200-95243800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:95242200-95244000	Enhancers	NH-A	brain
21	chr9:95242400-95243800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr9:95242400-95243800	Active TSS	Aorta	Aorta
23	chr9:95242400-95243800	Enhancers	Hela-S3	cervix
24	chr9:95242400-95243800	Enhancers	HSMMtube	muscle
25	chr9:95242400-95244000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr9:95242400-95244000	Active TSS	Fetal Muscle Trunk	muscle
27	chr9:95242400-95244000	Active TSS	Right Atrium	heart
28	chr9:95242400-95244000	Enhancers	HUVEC	blood vessel
29	chr9:95242400-95245200	Enhancers	Osteobl	bone
30	chr9:95242600-95243600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr9:95242600-95243600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr9:95242600-95243600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:95242600-95243600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:95242600-95243600	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr9:95242600-95243800	Enhancers	K562	blood
36	chr9:95242600-95243800	Enhancers	NHLF	lung
37	chr9:95242600-95244000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr9:95242600-95244000	Enhancers	HMEC	breast
39	chr9:95242600-95244200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:95242600-95247200	Enhancers	NHDF-Ad	bronchial
41	chr9:95242800-95243800	Enhancers	HSMM	muscle
42	chr9:95242800-95245200	Weak transcription	Fetal Intestine Small	intestine
43	chr9:95242800-95247200	Weak transcription	Left Ventricle	heart
44	chr9:95243000-95243600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr9:95243000-95243600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr9:95243000-95243800	Enhancers	H1 Cell Line	embryonic stem cell
47	chr9:95243000-95243800	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr9:95243000-95244000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr9:95243000-95244200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:95243000-95248200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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