Variant report

Variant	rs1196048
Chromosome Location	chr11:64842987-64842988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64807338..64809955-chr11:64842641..64845959,3	K562	blood:
2	chr11:64795265..64796796-chr11:64842573..64844398,2	K562	blood:
3	chr11:64842533..64844120-chr11:64877968..64880933,2	K562	blood:
4	chr11:64837451..64840290-chr11:64841461..64843514,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168061	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000149809	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];0.99[ASN][1000 genomes]
rs11227120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[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];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2458298	0.81[CEU][hapmap]
rs2507814	0.83[JPT][hapmap]
rs36057475	0.99[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];0.92[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];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs475089	0.91[EUR][1000 genomes]
rs477539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs484182	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496427	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs498636	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs502333	0.84[JPT][hapmap]
rs532373	0.96[CEU][hapmap];0.81[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];0.81[ASN][1000 genomes]
rs548150	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]
rs559644	0.81[ASN][1000 genomes]
rs564966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.83[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];0.81[ASN][1000 genomes]
rs7943007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[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];0.81[ASN][1000 genomes]
rs9971546	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[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
rs1196048	SCGB2A2	cis	cerebellum	SCAN
rs1196048	SNX15	cis	parietal	SCAN
rs1196048	RAB1B	cis	parietal	SCAN
rs1196048	SPDYC	cis	parietal	SCAN
rs1196048	RPS6KA4	cis	lymphoblastoid	GTEx
rs1196048	SNX15	cis	Muscle Skeletal	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64822400-64850800	Weak transcription	Esophagus	oesophagus
2	chr11:64833600-64845600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:64834200-64850600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:64834400-64845000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:64834600-64843000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:64834600-64846200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:64834800-64843000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:64834800-64843200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:64834800-64843400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:64834800-64843400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:64834800-64844800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:64834800-64845000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:64834800-64847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:64835000-64843000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:64835000-64843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:64835000-64843400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:64835200-64844000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:64835400-64843200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr11:64835400-64845000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:64835600-64843200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:64835800-64843000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:64836000-64843000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:64836600-64843200	Weak transcription	Fetal Stomach	stomach
24	chr11:64837000-64843200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:64837000-64843200	Weak transcription	NHEK	skin
26	chr11:64837200-64843400	Weak transcription	K562	blood
27	chr11:64837200-64844000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:64837400-64843400	Weak transcription	Fetal Thymus	thymus
29	chr11:64837400-64843600	Weak transcription	Fetal Intestine Small	intestine
30	chr11:64837400-64843800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr11:64837400-64844800	Weak transcription	Hela-S3	cervix
32	chr11:64837400-64848000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr11:64837600-64843200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:64837600-64843200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:64837600-64845000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:64837600-64845600	Weak transcription	Fetal Intestine Large	intestine
37	chr11:64837800-64843200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:64837800-64845000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr11:64837800-64845400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr11:64837800-64846800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:64837800-64850800	Weak transcription	Pancreas	Pancrea
42	chr11:64838000-64844200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:64839000-64844000	Weak transcription	NHLF	lung
44	chr11:64839400-64843400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr11:64839800-64847800	Weak transcription	HSMM	muscle
46	chr11:64840000-64843000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:64840200-64845000	Weak transcription	GM12878-XiMat	blood
48	chr11:64840200-64845600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr11:64840200-64850800	Weak transcription	Spleen	Spleen
50	chr11:64840400-64843000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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