Variant report

Variant	rs12729863
Chromosome Location	chr1:98000954-98000955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10875097	0.83[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12063030	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12093651	0.91[ASN][1000 genomes]
rs12138657	0.84[ASN][1000 genomes]
rs1415682	0.91[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs17116806	0.81[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs1801159	0.83[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs2297779	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297780	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2786518	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2786519	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2786771	0.83[ASW][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs2786772	0.87[ASN][1000 genomes]
rs2786774	0.91[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs2786778	0.91[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs2786780	0.91[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs2786785	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2811183	0.91[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs2811187	0.91[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs34934786	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4950040	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4950041	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4950042	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs952501	0.91[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv830703	chr1:97907708-98101144	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv933871	chr1:97981576-98003928	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12729863	AGL	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97872600-98014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:97928600-98018200	Weak transcription	Ovary	ovary
3	chr1:97956400-98009400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:97963000-98009400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:97964600-98010400	Weak transcription	Dnd41	blood
6	chr1:97976600-98014600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:97976600-98054200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:97976800-98009400	Weak transcription	Primary B cells from cord blood	blood
9	chr1:97976800-98051400	Weak transcription	Left Ventricle	heart
10	chr1:97980000-98013400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:97986600-98014600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:97987000-98003800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:97988200-98023000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:97990000-98013000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:97995800-98012000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:97996000-98037400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:97997000-98004400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:97997000-98009200	Weak transcription	HSMM	muscle
19	chr1:97998600-98063800	Weak transcription	Right Ventricle	heart
20	chr1:97998800-98012600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:97999000-98014600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:97999400-98064600	Weak transcription	Psoas Muscle	Psoas
23	chr1:97999400-98074000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:98000000-98003600	Weak transcription	Liver	Liver
25	chr1:98000200-98002000	Weak transcription	Primary T cells from cord blood	blood
26	chr1:98000800-98001800	Enhancers	HUVEC	blood vessel
27	chr1:98000800-98007800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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