Variant report

Variant	rs12436299
Chromosome Location	chr14:65785194-65785195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10131385	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10132229	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10135194	0.85[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10138151	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10144503	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145534	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10147958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10150168	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12431963	0.83[JPT][hapmap]
rs12433207	0.83[AMR][1000 genomes]
rs28557275	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28595734	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59233694	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7143109	0.81[JPT][hapmap]
rs73278053	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8010759	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs899961	0.81[JPT][hapmap]
rs9635250	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832817	chr14:65637069-65810406	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
2	nsv832818	chr14:65706859-65882320	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
5	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12436299	SIX1	cis	cerebellum	SCAN
rs12436299	SIX4	cis	cerebellum	SCAN
rs12436299	MAX	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65772400-65787800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr14:65779400-65787800	Weak transcription	Fetal Intestine Large	intestine
3	chr14:65781400-65786200	Weak transcription	Stomach Mucosa	stomach
4	chr14:65781600-65787600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr14:65781800-65785200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr14:65783600-65785600	Flanking Active TSS	Primary B cells from peripheral blood	blood
7	chr14:65784000-65785400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:65784000-65785400	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr14:65784000-65786000	Weak transcription	Small Intestine	intestine
10	chr14:65784200-65786800	Weak transcription	Fetal Intestine Small	intestine
11	chr14:65784200-65787400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr14:65784600-65785600	Enhancers	Fetal Thymus	thymus
13	chr14:65784600-65786400	Flanking Active TSS	GM12878-XiMat	blood
14	chr14:65784800-65785600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr14:65784800-65785600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr14:65784800-65785600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr14:65784800-65785800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr14:65784800-65786200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr14:65784800-65786600	Enhancers	Primary T cells from cord blood	blood
20	chr14:65785000-65786600	Weak transcription	Thymus	Thymus

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