Variant report

Variant	rs11169519
Chromosome Location	chr12:39177441-39177442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10161183	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10444553	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10506126	0.85[CEU][hapmap]
rs10783333	0.85[CEU][hapmap]
rs10875953	0.86[CEU][hapmap]
rs10876008	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs10876208	0.86[ASN][1000 genomes]
rs11169258	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs11169482	1.00[CEU][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes]
rs11169518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169535	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169616	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169760	0.91[ASN][1000 genomes]
rs11169768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12300353	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12314639	0.85[CEU][hapmap]
rs12424190	0.84[CEU][hapmap]
rs1386018	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs1400280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1400285	0.89[ASN][1000 genomes]
rs1403521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1516558	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1523118	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1523121	0.91[ASN][1000 genomes]
rs1586373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2388172	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs34246358	0.94[ASN][1000 genomes]
rs35749392	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759139	0.84[CEU][hapmap]
rs3803020	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3887436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4384412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4595586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4616077	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs4768388	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs56149694	0.92[ASN][1000 genomes]
rs56344858	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6580849	1.00[JPT][hapmap]
rs7309400	0.84[AFR][1000 genomes]
rs7312879	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7314227	0.92[ASN][1000 genomes]
rs7315271	0.96[CEU][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes]
rs7957376	0.90[JPT][hapmap]
rs7957999	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7960616	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs7960901	0.89[AFR][1000 genomes]
rs7962363	1.00[JPT][hapmap]
rs7970097	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7978766	0.81[AMR][1000 genomes]
rs7980448	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39153800-39188600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:39165800-39180600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:39166400-39178800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr12:39166600-39182000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:39168200-39180000	Weak transcription	Aorta	Aorta
6	chr12:39169400-39186600	Weak transcription	Hela-S3	cervix
7	chr12:39169600-39179600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:39169600-39182000	Weak transcription	Liver	Liver
9	chr12:39172200-39180000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:39176800-39177800	Enhancers	GM12878-XiMat	blood
11	chr12:39177000-39177600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr12:39177400-39188600	Weak transcription	Lung	lung

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