Variant report

Variant	rs10992796
Chromosome Location	chr9:96360905-96360906
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96356589..96359432-chr9:96360730..96362532,3	MCF-7	breast:
2	chr9:96353399..96355498-chr9:96360574..96362233,2	MCF-7	breast:
3	chr9:96360523..96363170-chr9:96791187..96793107,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158079	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1000850	0.80[CHD][hapmap]
rs1000852	0.83[CHD][hapmap]
rs10122092	0.81[CHD][hapmap]
rs10821170	0.89[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821171	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821172	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821177	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992794	0.92[ASN][1000 genomes]
rs10992795	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13290276	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13296529	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17533702	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254712	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2265300	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2265574	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265575	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265576	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2989752	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2989753	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2989755	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2989756	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2994365	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2994369	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2994370	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4073155	0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs4743929	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744255	0.87[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs4744258	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744259	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56351334	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62573991	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62574558	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs928368	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9409477	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9644969	0.83[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10992796	PTCH1	cis	parietal	SCAN
rs10992796	FAM120AOS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96341800-96362200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr9:96345000-96362600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr9:96349000-96365800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:96352400-96361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:96352400-96366000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:96352400-96369200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:96352400-96384600	Weak transcription	NHLF	lung
8	chr9:96352600-96362400	Weak transcription	Fetal Lung	lung
9	chr9:96354200-96361400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:96355000-96361800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:96355200-96362600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:96355200-96362800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:96355200-96362800	Weak transcription	Brain Angular Gyrus	brain
14	chr9:96355400-96361200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:96355400-96361400	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:96356400-96364000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr9:96356600-96365600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:96356800-96362600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:96357000-96361000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:96357000-96361000	Weak transcription	Gastric	stomach
21	chr9:96357000-96361200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:96357000-96361400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:96357000-96361400	Weak transcription	NHDF-Ad	bronchial
24	chr9:96357000-96361600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:96357000-96362200	Weak transcription	Small Intestine	intestine
26	chr9:96357000-96362400	Weak transcription	HSMM	muscle
27	chr9:96357000-96362600	Weak transcription	A549	lung
28	chr9:96357000-96367000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:96357200-96361200	Weak transcription	Stomach Mucosa	stomach
30	chr9:96357200-96361800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:96357200-96361800	Weak transcription	K562	blood
32	chr9:96357200-96362400	Weak transcription	Hela-S3	cervix
33	chr9:96357200-96362800	Weak transcription	HMEC	breast
34	chr9:96357400-96361000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:96357400-96362400	Weak transcription	NHEK	skin
36	chr9:96357600-96364200	Enhancers	Pancreas	Pancrea
37	chr9:96357600-96364600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:96357800-96362600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:96358200-96363000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr9:96358200-96363600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:96358400-96363000	Enhancers	Right Atrium	heart
42	chr9:96358400-96364000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr9:96358400-96365200	Enhancers	Primary B cells from peripheral blood	blood
44	chr9:96359000-96361000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr9:96359000-96361000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr9:96359000-96361200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr9:96359000-96361200	Weak transcription	Esophagus	oesophagus
48	chr9:96359200-96364000	Enhancers	Primary T cells fromperipheralblood	blood
49	chr9:96359400-96362600	Enhancers	Primary T cells from cord blood	blood
50	chr9:96359600-96361000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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