Variant report

Variant	rs12227809
Chromosome Location	chr12:45114329-45114330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10880664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11182546	1.00[CHB][hapmap]
rs11182547	1.00[CHB][hapmap]
rs11182553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182554	0.80[ASN][1000 genomes]
rs11182555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182564	0.80[ASN][1000 genomes]
rs11182565	0.80[ASN][1000 genomes]
rs11182566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182568	1.00[JPT][hapmap]
rs11182570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182575	1.00[JPT][hapmap]
rs11182576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182577	0.80[ASN][1000 genomes]
rs11182583	0.80[ASN][1000 genomes]
rs11182584	0.80[ASN][1000 genomes]
rs11182585	0.80[ASN][1000 genomes]
rs11182587	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182589	0.80[ASN][1000 genomes]
rs11182591	0.80[ASN][1000 genomes]
rs11182593	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11182594	0.90[ASN][1000 genomes]
rs11182600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182601	0.90[ASN][1000 genomes]
rs11182602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182610	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11182611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11182620	0.95[ASN][1000 genomes]
rs11182623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11182624	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11182625	0.80[ASN][1000 genomes]
rs11182626	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11182629	0.85[ASN][1000 genomes]
rs11182632	0.85[ASN][1000 genomes]
rs11182637	0.81[ASN][1000 genomes]
rs11182638	0.81[ASN][1000 genomes]
rs11182643	0.81[ASN][1000 genomes]
rs11182644	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11182645	0.81[ASN][1000 genomes]
rs11182646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11182648	0.81[ASN][1000 genomes]
rs11182649	0.81[ASN][1000 genomes]
rs11182651	0.81[ASN][1000 genomes]
rs11182652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11182653	1.00[JPT][hapmap]
rs11531203	0.90[ASN][1000 genomes]
rs12227198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12228607	0.81[ASN][1000 genomes]
rs12228891	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12229413	0.80[ASN][1000 genomes]
rs12229463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12230951	0.90[ASN][1000 genomes]
rs1452886	1.00[JPT][hapmap]
rs17094988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6582510	1.00[JPT][hapmap]
rs6582511	1.00[JPT][hapmap]
rs7961698	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv1049080	chr12:45097564-45195295	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45065000-45116000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:45080800-45136000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:45081400-45115600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:45105200-45117000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:45111000-45114400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:45111800-45120000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:45112800-45114600	Weak transcription	Fetal Brain Female	brain
8	chr12:45113400-45115400	Weak transcription	Fetal Brain Male	brain
9	chr12:45114000-45114800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:45114000-45115000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr12:45114200-45114400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:45114200-45114600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:45114200-45114600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr12:45114200-45114800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr12:45114200-45114800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:45114200-45114800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr12:45114200-45114800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:45114200-45115000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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