Variant report

Variant	rs67216675
Chromosome Location	chr3:49493151-49493152
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49491388..49494409-chr3:49505891..49508605,4	MCF-7	breast:
2	chr3:49492720..49494835-chr3:49497709..49500473,4	MCF-7	breast:
3	chr3:49493044..49494602-chr3:49495069..49497320,2	K562	blood:
4	chr3:49492642..49496554-chr3:49506266..49510118,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10212296	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1050088	0.82[ASN][1000 genomes]
rs1050450	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10640	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865955	0.94[ASN][1000 genomes]
rs11130193	0.83[ASN][1000 genomes]
rs11130196	0.90[ASN][1000 genomes]
rs11130199	0.82[ASN][1000 genomes]
rs11130202	0.82[ASN][1000 genomes]
rs11130203	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11706370	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11708955	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11711485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711536	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11712569	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11713474	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715915	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11716974	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11719996	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11720264	0.82[ASN][1000 genomes]
rs11720597	0.81[EUR][1000 genomes]
rs11922013	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11926781	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12330269	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489092	0.82[ASN][1000 genomes]
rs13062429	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13079082	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13079643	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13086611	0.84[AMR][1000 genomes]
rs13087851	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13090388	0.89[AMR][1000 genomes]
rs1568661	0.82[ASN][1000 genomes]
rs17080528	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1800668	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1801143	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1987628	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2312461	0.82[ASN][1000 genomes]
rs34196454	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34293138	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34363169	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34427167	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34588335	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35115732	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35169793	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35261698	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35701831	0.82[ASN][1000 genomes]
rs35999162	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811697	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3811699	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3870337	0.82[ASN][1000 genomes]
rs3870338	0.82[ASN][1000 genomes]
rs3877784	0.82[ASN][1000 genomes]
rs3924462	0.82[ASN][1000 genomes]
rs3926569	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4625	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855836	0.82[ASN][1000 genomes]
rs4855859	0.82[ASN][1000 genomes]
rs4855861	0.82[ASN][1000 genomes]
rs4855864	0.82[ASN][1000 genomes]
rs4855866	0.92[ASN][1000 genomes]
rs59152804	0.86[ASN][1000 genomes]
rs6446264	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6446272	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6446277	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67485053	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6766131	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766581	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6779524	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6793308	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6797664	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6809216	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6997	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71324962	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71615484	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7622302	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7623659	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7630869	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7633271	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637999	0.82[ASN][1000 genomes]
rs7643845	0.82[ASN][1000 genomes]
rs7645445	0.90[ASN][1000 genomes]
rs7646366	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648841	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs885592	0.94[ASN][1000 genomes]
rs9814873	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9818590	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9821311	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9827021	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9837027	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9841110	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850072	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9853683	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9858280	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858418	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9859556	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9871380	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9875617	0.82[EUR][1000 genomes]
rs9878943	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs67216675	FAM212A	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49482000-49498200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:49486600-49498600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:49490200-49494200	Enhancers	Fetal Muscle Trunk	muscle
4	chr3:49490600-49506600	Enhancers	Fetal Muscle Leg	muscle
5	chr3:49491200-49495000	Enhancers	Hela-S3	cervix
6	chr3:49491400-49493400	Enhancers	HepG2	liver
7	chr3:49491400-49494200	Enhancers	Right Ventricle	heart
8	chr3:49491800-49493800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr3:49491800-49494400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:49491800-49495000	Enhancers	HSMMtube	muscle
11	chr3:49491800-49506200	Enhancers	Placenta	Placenta
12	chr3:49492000-49493400	Enhancers	Adipose Nuclei	Adipose
13	chr3:49492000-49493400	Enhancers	Left Ventricle	heart
14	chr3:49492000-49493400	Enhancers	Psoas Muscle	Psoas
15	chr3:49492000-49493600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:49492000-49494000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:49492000-49494200	Enhancers	Fetal Heart	heart
18	chr3:49492000-49495000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:49492000-49495000	Enhancers	HSMM	muscle
20	chr3:49492200-49493200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:49492200-49493200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:49492200-49493200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:49492200-49493200	Enhancers	A549	lung
24	chr3:49492200-49494200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:49492200-49494200	Enhancers	HMEC	breast
26	chr3:49492200-49495000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:49492400-49493200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:49492400-49493200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:49492400-49493200	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr3:49492400-49493200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:49492400-49493200	Enhancers	Fetal Stomach	stomach
32	chr3:49492400-49493200	Enhancers	NHDF-Ad	bronchial
33	chr3:49492400-49493200	Enhancers	NHLF	lung
34	chr3:49492400-49493400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:49492400-49494200	Enhancers	Osteobl	bone
36	chr3:49492400-49495000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:49492600-49494200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:49492600-49494200	Enhancers	NHEK	skin
39	chr3:49492600-49498000	Weak transcription	Stomach Mucosa	stomach
40	chr3:49492800-49493200	Enhancers	Spleen	Spleen
41	chr3:49492800-49493800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:49492800-49496200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr3:49492800-49496200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:49492800-49496200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:49492800-49496200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:49492800-49496400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:49492800-49496400	Weak transcription	Fetal Kidney	kidney
48	chr3:49492800-49496400	Weak transcription	Lung	lung
49	chr3:49492800-49498800	Weak transcription	Right Atrium	heart
50	chr3:49492800-49499200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links