Variant report

Variant	rs11229601
Chromosome Location	chr11:58494339-58494340
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58488336..58491210-chr11:58491852..58494782,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10896818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896820	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896822	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229578	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229593	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229596	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229612	0.86[ASN][1000 genomes]
rs11229613	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229617	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11229618	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11229620	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11229623	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11229652	0.80[AMR][1000 genomes]
rs11229662	0.82[AMR][1000 genomes]
rs11530801	0.82[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12222236	0.80[AMR][1000 genomes]
rs12223073	0.93[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs12226395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12417075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12420969	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12421060	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17152916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938695	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938696	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938707	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1938713	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1938717	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1938730	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1941965	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1943277	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1943285	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1943305	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1954965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2105743	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2497377	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35649133	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3920943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4373954	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4418828	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs492795	0.80[AMR][1000 genomes]
rs511772	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs539567	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs542537	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs547654	0.80[AMR][1000 genomes]
rs550362	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55906811	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56000500	0.84[ASN][1000 genomes]
rs56073415	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56699801	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57121352	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572856	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60850183	0.82[AMR][1000 genomes]
rs614561	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs616779	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs675423	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs675757	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72925740	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72925778	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72927728	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72927767	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72929757	0.82[AMR][1000 genomes]
rs7951340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943655	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832168	chr11:58394060-58564651	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11229601	TMX2	cis	cerebellum	SCAN
rs11229601	OR5M11	cis	parietal	SCAN
rs11229601	FADS3	cis	cerebellum	SCAN
rs11229601	PATL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58492800-58495000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chr11:58492800-58495400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:58492800-58496800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr11:58493000-58494600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr11:58493000-58494800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr11:58493000-58494800	Enhancers	Adipose Nuclei	Adipose
7	chr11:58493000-58498200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr11:58493200-58494400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr11:58493200-58495000	Enhancers	Fetal Kidney	kidney
10	chr11:58493200-58495200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr11:58493200-58495400	Enhancers	Fetal Intestine Large	intestine
12	chr11:58493200-58496000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr11:58493400-58495400	Enhancers	Primary hematopoietic stem cells	blood
14	chr11:58493400-58495600	Enhancers	K562	blood
15	chr11:58493600-58495200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:58493600-58496800	Enhancers	Primary T cells from cord blood	blood
17	chr11:58493600-58497000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr11:58493800-58494600	Enhancers	Liver	Liver
19	chr11:58493800-58496000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr11:58493800-58496200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:58493800-58496800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr11:58494000-58495200	Enhancers	Thymus	Thymus
23	chr11:58494000-58495400	Enhancers	Fetal Intestine Small	intestine
24	chr11:58494200-58495200	Enhancers	Primary B cells from cord blood	blood
25	chr11:58494200-58495400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr11:58494200-58495600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr11:58494200-58495600	Enhancers	Primary B cells from peripheral blood	blood

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