Variant report

Variant	rs4544065
Chromosome Location	chr12:45108863-45108864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1037433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1037434	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10506256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10748400	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10785515	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10880655	0.93[CEU][hapmap]
rs10880657	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880658	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10880659	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10880660	0.89[ASN][1000 genomes]
rs10880666	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880673	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182552	0.85[YRI][hapmap]
rs11182556	0.80[YRI][hapmap]
rs11182559	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11182560	0.85[YRI][hapmap]
rs11182562	0.86[YRI][hapmap]
rs11182596	0.89[ASN][1000 genomes]
rs11182599	0.83[ASN][1000 genomes]
rs11182634	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11182635	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182636	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182640	0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12303497	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12312100	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12815257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563043	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1850406	0.87[CHD][hapmap];0.91[GIH][hapmap]
rs1869162	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2060839	0.86[YRI][hapmap]
rs2060840	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs2060841	0.86[YRI][hapmap]
rs2060842	0.86[YRI][hapmap]
rs2060895	0.84[ASW][hapmap];0.86[YRI][hapmap]
rs2060896	0.84[ASW][hapmap];0.85[YRI][hapmap]
rs2084843	0.87[ASN][1000 genomes]
rs2305448	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3858727	0.88[ASN][1000 genomes]
rs4768066	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768563	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs581473	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs583575	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs605722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615760	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs628408	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs632481	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs636843	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6582509	0.84[ASW][hapmap];0.86[YRI][hapmap]
rs678663	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688669	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7295999	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7299365	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs7300005	0.89[YRI][hapmap]
rs7301539	0.89[ASN][1000 genomes]
rs7308509	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7310844	0.89[ASN][1000 genomes]
rs7314643	0.88[ASN][1000 genomes]
rs7958389	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7958608	0.84[ASW][hapmap];0.86[YRI][hapmap]
rs7968076	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7970849	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs838973	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs966383	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs978540	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4544065	TMEM117	cis	parietal	SCAN

Chromatin state (count:17 , 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	chr12:45083200-45110000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:45088000-45110800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:45089000-45114200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:45090600-45110200	Weak transcription	Brain Germinal Matrix	brain
8	chr12:45091200-45110800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:45101200-45114000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr12:45104600-45109200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:45105200-45117000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:45105400-45111000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:45105800-45111200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr12:45106600-45110600	Weak transcription	Fetal Brain Female	brain
15	chr12:45106800-45110600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:45108400-45109400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:45108800-45109000	Enhancers	Fetal Brain Male	brain

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