Variant report

Variant	rs548150
Chromosome Location	chr11:64833935-64833936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64832671..64835759-chr11:64851097..64853512,3	MCF-7	breast:
2	chr11:64609376..64612087-chr11:64831542..64834071,2	MCF-7	breast:
3	chr11:64828596..64831631-chr11:64831856..64834174,3	K562	blood:
4	chr11:64781815..64785733-chr11:64830700..64833952,3	MCF-7	breast:
5	chr11:64813127..64817234-chr11:64832954..64835448,4	MCF-7	breast:
6	chr11:64830399..64834355-chr11:64844286..64848376,4	K562	blood:
7	chr11:64832014..64834014-chr11:64836154..64838250,2	K562	blood:

Variant related genes	Relation type
ENSG00000162300	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000168060	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11227118	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11227120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11231929	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1196048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2458298	0.81[CEU][hapmap]
rs2507814	0.83[JPT][hapmap]
rs36057475	0.96[ASN][1000 genomes]
rs3782094	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3802936	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3825073	0.86[CHB][hapmap]
rs3862374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs475089	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs477539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs484182	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs486984	0.82[JPT][hapmap]
rs489489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs496427	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498636	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs502333	0.84[JPT][hapmap]
rs532373	0.96[CEU][hapmap];0.83[ASN][1000 genomes]
rs534236	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs559644	0.83[ASN][1000 genomes]
rs564966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs566908	0.87[ASW][hapmap]
rs653111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591869	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs7943007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs947799	0.92[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs9971546	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs548150	SNX15	cis	Muscle Skeletal	GTEx
rs548150	SNX15	cis	parietal	SCAN
rs548150	RPS6KA4	cis	lymphoblastoid	GTEx
rs548150	SPDYC	cis	parietal	SCAN
rs548150	SCGB2A2	cis	cerebellum	SCAN
rs548150	RAB1B	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64822400-64850800	Weak transcription	Esophagus	oesophagus
2	chr11:64828600-64834400	Weak transcription	Fetal Thymus	thymus
3	chr11:64830000-64834000	Weak transcription	GM12878-XiMat	blood
4	chr11:64830000-64836800	Weak transcription	Spleen	Spleen
5	chr11:64830200-64835800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr11:64830800-64835600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr11:64831400-64835400	Enhancers	Fetal Intestine Large	intestine
8	chr11:64833200-64834000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:64833200-64834000	Enhancers	Fetal Intestine Small	intestine
10	chr11:64833200-64834600	Enhancers	K562	blood
11	chr11:64833200-64834800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:64833200-64835000	Flanking Active TSS	HepG2	liver
13	chr11:64833400-64834600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr11:64833400-64835800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr11:64833600-64834000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr11:64833600-64834000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr11:64833600-64834400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:64833600-64834600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:64833600-64834800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:64833600-64835400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:64833600-64845600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr11:64833800-64834000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:64833800-64834000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr11:64833800-64834400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:64833800-64834600	Enhancers	H9 Cell Line	embryonic stem cell
26	chr11:64833800-64834800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr11:64833800-64834800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:64833800-64834800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:64833800-64834800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:64833800-64835000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr11:64833800-64835400	Enhancers	HUES64 Cell Line	embryonic stem cell

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