Variant report

Variant	rs7849752
Chromosome Location	chr9:96391990-96391991
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96382620..96384260-chr9:96389901..96392114,2	MCF-7	breast:
2	chr9:96391172..96393560-chr9:96396943..96399376,2	K562	blood:
3	chr9:96391831..96394155-chr9:96413684..96415869,2	K562	blood:
4	chr9:96338187..96341203-chr9:96391174..96393981,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197724	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10761245	0.95[CHB][hapmap]
rs10761247	0.82[CHB][hapmap]
rs10761249	0.91[CHB][hapmap]
rs10761254	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs10821184	0.83[CHB][hapmap]
rs10821191	0.91[CHB][hapmap]
rs10821196	0.87[CHB][hapmap]
rs10992807	0.87[CHB][hapmap]
rs10992854	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs11534279	0.95[CHB][hapmap]
rs11793637	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12002044	0.95[CHB][hapmap]
rs1806458	0.87[CHB][hapmap]
rs2001589	0.95[CHB][hapmap]
rs2001994	0.83[CHB][hapmap]
rs2398849	0.98[ASN][1000 genomes]
rs2398855	0.82[CHB][hapmap]
rs2398856	0.95[CHB][hapmap]
rs3750354	0.95[CHB][hapmap]
rs3750358	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs3750361	0.93[ASN][1000 genomes]
rs3750362	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs4403473	0.94[ASN][1000 genomes]
rs4744263	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479499	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs7018598	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7024028	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs7851178	0.91[CHB][hapmap]
rs7864397	0.91[CHB][hapmap]
rs7868191	0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040891	chr9:96361529-96397338	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1044461	chr9:96362048-96397338	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv893585	chr9:96363859-96403367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1055035	chr9:96372269-96402747	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv519449	chr9:96382100-96395429	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7849752	PTCH1	cis	parietal	SCAN
rs7849752	FAM120A	cis	parietal	SCAN
rs7849752	FAM120AOS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96363200-96392000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:96372800-96392000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:96374600-96399800	Weak transcription	K562	blood
4	chr9:96376200-96393000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:96380200-96411800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:96380800-96399800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:96384000-96396400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:96384600-96393600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:96384600-96412200	Weak transcription	Stomach Mucosa	stomach
10	chr9:96385400-96392000	Weak transcription	Pancreas	Pancrea
11	chr9:96385800-96392200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:96386400-96392200	Weak transcription	Ovary	ovary
13	chr9:96386600-96392200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:96386800-96392000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:96387000-96411800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:96387200-96392400	Weak transcription	Left Ventricle	heart
17	chr9:96387200-96399800	Weak transcription	Fetal Heart	heart
18	chr9:96387600-96399600	Weak transcription	Fetal Kidney	kidney
19	chr9:96390200-96398800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr9:96390200-96405400	Weak transcription	HepG2	liver
21	chr9:96390400-96392000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:96390400-96392000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:96390400-96392000	Weak transcription	Spleen	Spleen
24	chr9:96390400-96392200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:96390400-96392400	Weak transcription	Liver	Liver
26	chr9:96390400-96393400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:96390400-96395200	Weak transcription	NHLF	lung
28	chr9:96390400-96398600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:96390400-96399400	Weak transcription	Hela-S3	cervix
30	chr9:96390600-96392000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr9:96390600-96392000	Weak transcription	Esophagus	oesophagus
32	chr9:96390600-96392000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr9:96390600-96392000	Weak transcription	Dnd41	blood
34	chr9:96390600-96392200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:96390600-96392400	Weak transcription	Brain Angular Gyrus	brain
36	chr9:96390600-96392400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:96390600-96392400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr9:96390600-96392800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:96390600-96393200	Weak transcription	GM12878-XiMat	blood
40	chr9:96390600-96393400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:96390600-96393400	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:96390600-96393800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:96390600-96393800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:96390600-96395200	Weak transcription	Brain Substantia Nigra	brain
45	chr9:96390600-96397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:96390600-96398200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr9:96390600-96398400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:96390600-96399000	Weak transcription	Osteobl	bone
49	chr9:96390600-96399600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:96390800-96392000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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