Variant report

Variant	rs11229555
Chromosome Location	chr11:58408687-58408688
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:58385876..58387982-chr11:58406021..58408836,2	MCF-7	breast:
2	chr11:58408491..58410275-chr11:58912566..58915086,2	K562	blood:
3	chr11:58396664..58398524-chr11:58408556..58410829,2	K562	blood:
4	chr11:58405749..58408727-chr11:58417141..58419096,2	K562	blood:
5	chr11:58402930..58405768-chr11:58406418..58410060,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10896785	0.81[AMR][1000 genomes]
rs10896787	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896788	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896794	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896795	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896796	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229463	1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11229505	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11229512	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229519	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229543	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11229545	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11601687	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11603890	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605269	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605297	0.91[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11605683	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12787765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12799215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12800710	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12808544	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17567523	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1938598	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275993	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298608	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3168135	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7102510	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7102852	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7110210	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7925560	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7927966	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8373	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1050444	chr11:58404467-58434568	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11229555	MS4A10	cis	cerebellum	SCAN
rs11229555	OR4C6	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58406000-58410200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:58406200-58411200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:58406200-58413000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:58406600-58409200	Enhancers	Brain Hippocampus Middle	brain
5	chr11:58406800-58409000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr11:58407000-58408800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr11:58407000-58408800	Enhancers	Brain Angular Gyrus	brain
8	chr11:58407000-58408800	Enhancers	Thymus	Thymus
9	chr11:58407000-58409000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr11:58407000-58409000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr11:58407000-58409000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr11:58407000-58409000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr11:58407000-58409000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:58407000-58409200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:58407200-58408800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr11:58407200-58408800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:58407200-58408800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr11:58407200-58408800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr11:58407200-58408800	Enhancers	Spleen	Spleen
20	chr11:58407200-58408800	Enhancers	Dnd41	blood
21	chr11:58407200-58409200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:58407200-58409600	Enhancers	Primary hematopoietic stem cells	blood
23	chr11:58407200-58410000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr11:58407400-58408800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr11:58407400-58408800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr11:58407400-58408800	Enhancers	Brain Cingulate Gyrus	brain
27	chr11:58407400-58408800	Enhancers	Brain Substantia Nigra	brain
28	chr11:58407400-58409000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:58407600-58410800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr11:58407800-58410400	Enhancers	Fetal Intestine Large	intestine
31	chr11:58407800-58410600	Enhancers	Fetal Intestine Small	intestine
32	chr11:58408000-58408800	Enhancers	Ovary	ovary
33	chr11:58408000-58410000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:58408200-58408800	Enhancers	Colonic Mucosa	Colon
35	chr11:58408200-58409800	Enhancers	Duodenum Mucosa	Duodenum
36	chr11:58408400-58408800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr11:58408400-58409000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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