Variant report

Variant	rs10875935
Chromosome Location	chr12:49609166-49609167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49607696..49610266-chr12:49612942..49614601,2	K562	blood:
2	chr12:49523661..49526091-chr12:49606547..49609332,3	MCF-7	breast:
3	chr12:49580930..49584417-chr12:49606768..49610900,5	MCF-7	breast:
4	chr12:49523075..49526693-chr12:49608220..49614713,7	K562	blood:
5	chr12:49608287..49610880-chr12:49615814..49620950,5	K562	blood:
6	chr12:49608287..49611416-chr12:49615384..49618103,4	K562	blood:

Variant related genes	Relation type
ENSG00000258017	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10747563	0.84[CHB][hapmap]
rs10875934	0.84[CHB][hapmap]
rs11168920	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168921	1.00[ASN][1000 genomes]
rs11168924	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34022807	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34367716	0.90[ASN][1000 genomes]
rs68128447	0.89[ASN][1000 genomes]
rs7306084	0.84[CHB][hapmap]
rs7959497	0.84[CHB][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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10875935	OR10AD1	cis	parietal	SCAN
rs10875935	OR10AD1	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49606400-49610200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:49606600-49609200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:49606600-49609600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr12:49606600-49610000	Enhancers	NHLF	lung
5	chr12:49606800-49609400	Enhancers	A549	lung
6	chr12:49606800-49609400	Enhancers	NHDF-Ad	bronchial
7	chr12:49607200-49609200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:49607200-49609400	Enhancers	Rectal Smooth Muscle	rectum
9	chr12:49607200-49609400	Enhancers	Osteobl	bone
10	chr12:49607200-49610000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:49607200-49610000	Enhancers	NH-A	brain
12	chr12:49607400-49609200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr12:49607600-49609400	Enhancers	Fetal Kidney	kidney
14	chr12:49607600-49610200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:49607600-49611000	Enhancers	Fetal Brain Male	brain
16	chr12:49607800-49609400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:49607800-49609600	Enhancers	Fetal Muscle Trunk	muscle
18	chr12:49607800-49612200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr12:49608000-49616400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:49608400-49609200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49608400-49609200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr12:49608400-49609200	Enhancers	Right Atrium	heart
23	chr12:49608400-49609400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:49608400-49609400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:49608400-49609400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:49608400-49609400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:49608400-49609400	Enhancers	Adipose Nuclei	Adipose
28	chr12:49608400-49609400	Enhancers	Fetal Heart	heart
29	chr12:49608400-49609400	Enhancers	Fetal Lung	lung
30	chr12:49608400-49609400	Enhancers	Fetal Stomach	stomach
31	chr12:49608400-49609400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:49608400-49609400	Enhancers	Hela-S3	cervix
33	chr12:49608400-49610000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr12:49608400-49610200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr12:49608400-49610200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr12:49608400-49610200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:49608400-49610200	Enhancers	Fetal Muscle Leg	muscle
38	chr12:49608600-49609200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr12:49608600-49609200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr12:49608600-49609200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr12:49608600-49609200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr12:49608600-49609200	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr12:49608600-49609200	Enhancers	Colonic Mucosa	Colon
44	chr12:49608600-49609200	Enhancers	Fetal Intestine Small	intestine
45	chr12:49608600-49609200	Enhancers	Placenta	Placenta
46	chr12:49608600-49609200	Enhancers	Left Ventricle	heart
47	chr12:49608600-49609400	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr12:49608600-49609400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr12:49608600-49609400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr12:49608600-49609400	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links