Variant report

Variant	rs1144410
Chromosome Location	chr11:105780125-105780126
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1043144	0.82[YRI][hapmap]
rs11226908	0.83[JPT][hapmap]
rs1267444	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs1939153	0.83[ASW][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1939800	0.84[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap]
rs3758790	0.82[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs471396	0.84[JPT][hapmap]
rs471795	0.82[JPT][hapmap]
rs505829	0.82[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs507450	0.84[JPT][hapmap]
rs509512	0.83[ASW][hapmap];0.85[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs511106	0.83[JPT][hapmap]
rs539238	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs541640	0.84[JPT][hapmap]
rs548814	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs556968	0.84[JPT][hapmap]
rs561643	0.84[JPT][hapmap]
rs567161	0.82[ASN][1000 genomes]
rs571533	0.82[ASN][1000 genomes]
rs587978	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588638	0.82[ASN][1000 genomes]
rs589104	0.88[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs593130	0.82[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs596100	0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs601480	0.82[ASW][hapmap];0.82[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs609235	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs609665	0.95[LWK][hapmap];0.93[YRI][hapmap]
rs619323	0.82[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs622178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622367	0.84[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs631002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638777	0.81[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs639003	0.85[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs641574	0.86[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap]
rs645905	0.85[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs649098	0.83[GIH][hapmap]
rs654035	0.84[JPT][hapmap]
rs656292	0.84[JPT][hapmap]
rs665554	0.84[JPT][hapmap]
rs667174	0.81[MKK][hapmap]
rs669397	0.83[ASW][hapmap];0.85[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs669793	0.85[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs675001	0.82[ASN][1000 genomes]
rs681156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs685725	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs694514	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[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	nsv832257	chr11:105662753-105817576	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1144410	TMEM123	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105771400-105785600	Weak transcription	Brain Angular Gyrus	brain
2	chr11:105774200-105784400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:105774200-105785600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:105777000-105780400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:105778200-105780800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:105778200-105781000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:105778400-105785600	Weak transcription	Brain Substantia Nigra	brain

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