Variant report

Variant	rs41623
Chromosome Location	chr7:120428799-120428800
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120415321..120417189-chr7:120427824..120430329,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10266755	0.91[CEU][hapmap]
rs10274689	0.81[CEU][hapmap]
rs114420	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11976580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12154976	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12673417	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17132731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17142976	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17143013	0.93[ASN][1000 genomes]
rs2107275	0.86[CEU][hapmap]
rs2189974	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2525706	0.81[ASN][1000 genomes]
rs2525710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2721329	0.81[ASN][1000 genomes]
rs2721330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2721332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2721344	0.93[ASN][1000 genomes]
rs2721346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2721348	0.93[ASN][1000 genomes]
rs2721360	0.93[ASN][1000 genomes]
rs2721371	0.93[ASN][1000 genomes]
rs3823861	0.95[CEU][hapmap]
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	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41617	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41619	0.86[EUR][1000 genomes]
rs41620	0.88[EUR][1000 genomes]
rs41621	0.83[EUR][1000 genomes]
rs41622	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41624	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs41626	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41628	0.83[EUR][1000 genomes]
rs41629	0.86[CEU][hapmap]
rs41632	0.95[CEU][hapmap]
rs42333	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[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	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6953454	0.81[CEU][hapmap]
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	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810542	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs886440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[ASN][1000 genomes]
rs996903	0.81[CEU][hapmap]

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
rs41623	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:26 , 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	chr7:120425600-120433200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:120425600-120434400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:120425600-120434400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:120425600-120470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:120425800-120432400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:120425800-120434800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:120425800-120437600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:120425800-120454400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:120426000-120429200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:120426000-120432000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr7:120426200-120432000	Weak transcription	Fetal Heart	heart
13	chr7:120426400-120429600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr7:120426400-120431200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr7:120426600-120442000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr7:120426800-120432200	Weak transcription	Fetal Intestine Large	intestine
17	chr7:120427000-120428800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr7:120427400-120432200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:120427400-120466000	Weak transcription	Fetal Stomach	stomach
20	chr7:120427800-120432000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:120427800-120432400	Weak transcription	Fetal Kidney	kidney
22	chr7:120427800-120438400	Weak transcription	Aorta	Aorta
23	chr7:120428200-120429400	Strong transcription	Fetal Muscle Leg	muscle
24	chr7:120428200-120429400	Strong transcription	Left Ventricle	heart
25	chr7:120428400-120430200	Strong transcription	Liver	Liver
26	chr7:120428400-120440400	Weak transcription	Fetal Intestine Small	intestine

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