Variant report

Variant	rs2458298
Chromosome Location	chr11:64814813-64814814
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64812307-64815018	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr11:64814587-64815278	HepG2	liver:	n/a	n/a
3	ELF1	chr11:64814808-64815479	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64807810..64812277-chr11:64813364..64817609,8	MCF-7	breast:
2	chr11:64814122..64816678-chr11:65265607..65267659,2	MCF-7	breast:
3	chr11:64813509..64815551-chr11:64854732..64857551,2	K562	blood:
4	chr11:64813127..64817234-chr11:64832954..64835448,4	MCF-7	breast:

Variant related genes	Relation type
NAALADL1	TF binding region
ENSG00000146670	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000187066	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000168061	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10897544	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231929	0.81[CEU][hapmap]
rs1196048	0.81[CEU][hapmap]
rs1300845	0.94[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2507814	0.95[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3741390	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3759041	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs3850947	0.95[GIH][hapmap];0.84[TSI][hapmap]
rs3862374	0.81[CEU][hapmap]
rs476824	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs477539	0.84[CEU][hapmap]
rs486984	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs488686	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs489489	0.81[CEU][hapmap]
rs502333	0.88[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs525433	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs533018	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs548150	0.81[CEU][hapmap]
rs562590	0.94[ASW][hapmap];0.87[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs564966	0.80[CEU][hapmap]
rs566221	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs613874	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs620981	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs653111	0.81[CEU][hapmap]
rs678614	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897709	chr11:64772545-64870779	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
5	esv2334525	chr11:64814812-64814814	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2458298	SNX15	cis	parietal	SCAN
rs2458298	SPDYC	cis	parietal	SCAN
rs2458298	B3GAT3	cis	cerebellum	SCAN
rs2458298	SCGB2A2	cis	cerebellum	SCAN
rs2458298	SNX15	cis	Muscle Skeletal	GTEx
rs2458298	LRRN4CL	cis	parietal	SCAN
rs2458298	SNX15	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64812600-64815600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr11:64812600-64815800	Weak transcription	A549	lung
3	chr11:64812600-64820200	Weak transcription	HMEC	breast
4	chr11:64813000-64815400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr11:64813000-64815600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:64813000-64815800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:64813200-64815000	Weak transcription	HSMM	muscle
8	chr11:64813200-64816800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:64813400-64815000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr11:64813400-64818400	Weak transcription	K562	blood
11	chr11:64813400-64821200	Weak transcription	Primary T cells from cord blood	blood
12	chr11:64813400-64824200	Weak transcription	HepG2	liver
13	chr11:64813800-64815400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:64813800-64815600	Weak transcription	Dnd41	blood
15	chr11:64813800-64815800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:64813800-64816000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr11:64813800-64816000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:64813800-64818600	Weak transcription	Hela-S3	cervix
19	chr11:64813800-64833200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:64814000-64815000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:64814000-64815000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:64814000-64815200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr11:64814000-64815400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:64814000-64816000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:64814000-64816200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:64814000-64827600	Weak transcription	Pancreas	Pancrea
27	chr11:64814200-64815000	Enhancers	Liver	Liver
28	chr11:64814200-64816000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:64814200-64818000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:64814400-64815000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:64814400-64815000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr11:64814400-64815000	Weak transcription	Thymus	Thymus
33	chr11:64814400-64815200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:64814600-64815000	Enhancers	Primary B cells from cord blood	blood
35	chr11:64814600-64815000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:64814600-64815000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr11:64814600-64815000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr11:64814600-64815000	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr11:64814600-64815000	Enhancers	Spleen	Spleen
40	chr11:64814600-64815000	Enhancers	NHEK	skin
41	chr11:64814600-64815200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr11:64814600-64815200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:64814600-64815200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr11:64814600-64815400	Active TSS	Ovary	ovary
45	chr11:64814600-64815600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr11:64814600-64815600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:64814600-64815600	Active TSS	NHDF-Ad	bronchial
48	chr11:64814600-64815800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:64814600-64815800	Active TSS	Brain Angular Gyrus	brain
50	chr11:64814600-64815800	Active TSS	Rectal Mucosa Donor 29	rectum

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