Variant report

Variant	rs41626
Chromosome Location	chr7:120437607-120437608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120431634..120433947-chr7:120435928..120437734,2	K562	blood:
2	chr7:120437232..120440783-chr7:120445669..120448518,3	K562	blood:
3	chr7:120435241..120438206-chr7:120589721..120591272,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs114420	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11976580	0.93[ASN][1000 genomes]
rs12154976	0.95[EUR][1000 genomes]
rs12673417	1.00[ASN][1000 genomes]
rs17132731	0.93[ASN][1000 genomes]
rs17142976	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17143013	0.93[ASN][1000 genomes]
rs2189974	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2525706	0.81[ASN][1000 genomes]
rs2525710	0.81[ASN][1000 genomes]
rs2721329	0.81[ASN][1000 genomes]
rs2721330	0.81[ASN][1000 genomes]
rs2721332	0.93[ASN][1000 genomes]
rs2721344	0.93[ASN][1000 genomes]
rs2721346	0.93[ASN][1000 genomes]
rs2721348	0.93[ASN][1000 genomes]
rs2721360	0.93[ASN][1000 genomes]
rs2721371	0.93[ASN][1000 genomes]
rs41612	0.94[EUR][1000 genomes]
rs41613	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41614	0.87[EUR][1000 genomes]
rs41616	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41617	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41619	0.86[EUR][1000 genomes]
rs41620	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41621	0.83[EUR][1000 genomes]
rs41622	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41623	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41624	0.83[EUR][1000 genomes]
rs41628	0.83[EUR][1000 genomes]
rs42333	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730982	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55733320	1.00[ASN][1000 genomes]
rs55749650	0.88[ASN][1000 genomes]
rs56023697	0.93[ASN][1000 genomes]
rs56067931	1.00[ASN][1000 genomes]
rs61481874	0.93[ASN][1000 genomes]
rs67679138	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73427871	0.93[ASN][1000 genomes]
rs73427873	0.93[ASN][1000 genomes]
rs73427878	0.93[ASN][1000 genomes]
rs73721472	0.94[ASN][1000 genomes]
rs7805733	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810542	1.00[ASN][1000 genomes]
rs886440	1.00[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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41626	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120423000-120449200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:120425600-120470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:120425800-120454400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:120426600-120442000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr7:120427400-120466000	Weak transcription	Fetal Stomach	stomach
6	chr7:120427800-120438400	Weak transcription	Aorta	Aorta
7	chr7:120428400-120440400	Weak transcription	Fetal Intestine Small	intestine
8	chr7:120429200-120445600	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:120430400-120468200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:120432400-120442200	Weak transcription	Right Ventricle	heart
11	chr7:120432600-120438000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:120432600-120438200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:120432600-120438800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:120432600-120444600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:120432600-120453800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:120432600-120455400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:120432600-120468400	Weak transcription	Lung	lung
18	chr7:120432800-120438800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:120433200-120446000	Weak transcription	Fetal Kidney	kidney
20	chr7:120436200-120445600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:120437000-120437800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
22	chr7:120437000-120444800	Weak transcription	Left Ventricle	heart
23	chr7:120437200-120437800	ZNF genes & repeats	Liver	Liver
24	chr7:120437200-120437800	ZNF genes & repeats	Fetal Muscle Leg	muscle
25	chr7:120437200-120441400	Strong transcription	Fetal Intestine Large	intestine
26	chr7:120437400-120437800	ZNF genes & repeats	HSMMtube	muscle
27	chr7:120437600-120437800	Enhancers	Fetal Heart	heart
28	chr7:120437600-120438000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:120437600-120439400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:120437600-120439400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links