Variant report

Variant	rs10761237
Chromosome Location	chr9:96340817-96340818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:101964530..101966057-chr9:96338377..96341052,2	MCF-7	breast:
2	chr9:96207292..96208805-chr9:96339241..96341688,2	MCF-7	breast:
3	chr9:95818234..95820974-chr9:96339140..96341685,2	MCF-7	breast:
4	chr15:64672393..64674955-chr9:96338463..96341441,2	MCF-7	breast:
5	chr9:96340603..96342904-chr9:96370807..96373306,2	K562	blood:
6	chr9:96213158..96214882-chr9:96338001..96341678,3	K562	blood:
7	chr9:96211528..96214948-chr9:96337573..96343441,10	MCF-7	breast:
8	chr9:96211672..96218862-chr9:96335264..96341672,16	MCF-7	breast:
9	chr9:96298295..96300963-chr9:96339660..96341258,2	MCF-7	breast:
10	chr9:96289339..96291734-chr9:96339194..96341014,2	MCF-7	breast:
11	chr9:96323290..96325963-chr9:96339113..96341830,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000166803	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10115234	0.87[ASW][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10429558	0.81[YRI][hapmap]
rs10761234	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10821126	0.82[AMR][1000 genomes]
rs10821131	0.83[AMR][1000 genomes]
rs10821135	0.85[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes]
rs10821144	0.92[AMR][1000 genomes]
rs10821155	0.85[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10821162	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10821171	0.81[CHB][hapmap]
rs10992783	0.88[ASN][1000 genomes]
rs10992788	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992789	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11975	0.81[YRI][hapmap]
rs13292712	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2184255	0.80[ASW][hapmap]
rs2989753	0.81[CHB][hapmap]
rs3901421	0.92[YRI][hapmap];0.89[AMR][1000 genomes]
rs3933795	0.87[ASW][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes]
rs4237221	0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4310267	0.81[AMR][1000 genomes]
rs4607675	0.86[AMR][1000 genomes]
rs4743927	0.92[AMR][1000 genomes]
rs4744243	0.85[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs4744245	0.87[AMR][1000 genomes]
rs61707921	0.85[AMR][1000 genomes]
rs6479484	0.80[ASW][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes]
rs6479485	0.90[AMR][1000 genomes]
rs6479492	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479493	0.82[MEX][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7019001	0.85[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7020852	0.80[ASW][hapmap]
rs7021689	0.86[AMR][1000 genomes]
rs7023212	0.91[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7023577	0.87[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7035504	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7040832	0.89[AMR][1000 genomes]
rs7860098	0.81[YRI][hapmap]
rs883782	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs883784	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs952288	0.85[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes]
rs966789	0.91[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[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	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10761237	FAM120A	cis	cerebellum	SCAN
rs10761237	FAM120AOS	Cis_1M	lymphoblastoid	RTeQTL
rs10761237	FAM120AOS	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96337600-96341000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr9:96338000-96341000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:96339800-96341000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:96339800-96341000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:96339800-96341000	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr9:96339800-96341000	Flanking Active TSS	Dnd41	blood
7	chr9:96339800-96341000	Flanking Active TSS	GM12878-XiMat	blood
8	chr9:96339800-96341400	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr9:96339800-96341600	Flanking Active TSS	Fetal Brain Female	brain
10	chr9:96340000-96341000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:96340000-96341000	Flanking Active TSS	HepG2	liver
12	chr9:96340000-96341400	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr9:96340000-96344400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr9:96340200-96341000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr9:96340200-96341400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr9:96340200-96341600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:96340200-96342200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:96340200-96342400	Enhancers	Fetal Brain Male	brain
19	chr9:96340400-96341000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr9:96340400-96341000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:96340400-96341000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:96340400-96341000	Enhancers	Ovary	ovary
23	chr9:96340400-96341400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:96340400-96341400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr9:96340400-96341400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr9:96340400-96341400	Enhancers	Small Intestine	intestine
27	chr9:96340400-96344000	Weak transcription	Aorta	Aorta
28	chr9:96340400-96344200	Weak transcription	K562	blood
29	chr9:96340400-96344800	Enhancers	Gastric	stomach
30	chr9:96340400-96344800	Enhancers	Spleen	Spleen
31	chr9:96340400-96345200	Enhancers	Liver	Liver
32	chr9:96340400-96345600	Enhancers	Stomach Mucosa	stomach
33	chr9:96340400-96348200	Weak transcription	Fetal Kidney	kidney
34	chr9:96340400-96351200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:96340600-96341000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:96340600-96341000	Enhancers	Colonic Mucosa	Colon
37	chr9:96340600-96341000	Enhancers	Fetal Heart	heart
38	chr9:96340600-96341000	Enhancers	Fetal Stomach	stomach
39	chr9:96340600-96341000	Enhancers	Psoas Muscle	Psoas
40	chr9:96340600-96341000	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr9:96340600-96341000	Enhancers	Right Atrium	heart
42	chr9:96340600-96341000	Enhancers	A549	lung
43	chr9:96340600-96341000	Enhancers	HMEC	breast
44	chr9:96340600-96341000	Enhancers	NHEK	skin
45	chr9:96340600-96341200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr9:96340600-96341200	Enhancers	Fetal Thymus	thymus
47	chr9:96340600-96341200	Enhancers	NHDF-Ad	bronchial
48	chr9:96340600-96341400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr9:96340600-96341400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr9:96340600-96341400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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