Variant report

Variant	rs2509929
Chromosome Location	chr11:58407073-58407074
allele	A/C
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	chr11:58344813..58346955-chr11:58405857..58408185,2	MCF-7	breast:
3	chr11:58402145..58403700-chr11:58406157..58408220,2	K562	blood:
4	chr11:58405749..58408727-chr11:58417141..58419096,2	K562	blood:
5	chr11:58402930..58405768-chr11:58406418..58410060,3	K562	blood:

Variant related genes	Relation type
ENSG00000255073	Chromatin interaction
ENSG00000110031	Chromatin interaction
ENSG00000186660	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10750899	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10750900	1.00[EUR][1000 genomes]
rs11827157	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12277283	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12292248	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1802347	1.00[EUR][1000 genomes]
rs1944053	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs2507759	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2509917	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs2509921	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2509926	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2510549	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs2510551	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2510556	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs2510558	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2510862	1.00[EUR][1000 genomes]
rs2510863	0.84[EUR][1000 genomes]
rs2515348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs2515349	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2515358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2515360	1.00[EUR][1000 genomes]
rs2515361	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs2515372	1.00[EUR][1000 genomes]
rs55867213	1.00[EUR][1000 genomes]
rs55952041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56233432	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591480	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs7358405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7928565	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs7930253	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2509929	LPXN	cis	multi-tissue	Pritchard
rs2509929	GPR3	trans	brain	seeQTL
rs2509929	DUSP2	trans	brain	seeQTL
rs2509929	FCER2	trans	brain	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58393000-58407200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr11:58393800-58407800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:58394000-58407200	Weak transcription	Left Ventricle	heart
4	chr11:58394000-58407800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:58394600-58407200	Weak transcription	Primary T cells from cord blood	blood
6	chr11:58394600-58407200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr11:58394800-58408200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:58395600-58407200	Weak transcription	Dnd41	blood
9	chr11:58395800-58407800	Weak transcription	Fetal Thymus	thymus
10	chr11:58402400-58407800	Weak transcription	Fetal Intestine Small	intestine
11	chr11:58403600-58407200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:58404400-58408000	Weak transcription	Ovary	ovary
13	chr11:58405200-58407800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:58406000-58407600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:58406000-58410200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:58406200-58408200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr11:58406200-58411200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:58406200-58413000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:58406600-58409200	Enhancers	Brain Hippocampus Middle	brain
20	chr11:58406800-58409000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr11:58407000-58407200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:58407000-58407400	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr11:58407000-58408200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:58407000-58408400	Enhancers	Brain Anterior Caudate	brain
25	chr11:58407000-58408800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr11:58407000-58408800	Enhancers	Brain Angular Gyrus	brain
27	chr11:58407000-58408800	Enhancers	Thymus	Thymus
28	chr11:58407000-58409000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr11:58407000-58409000	Enhancers	Primary T cells fromperipheralblood	blood
30	chr11:58407000-58409000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr11:58407000-58409000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr11:58407000-58409000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:58407000-58409200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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