Variant report

Variant	rs565198
Chromosome Location	chr11:65913508-65913509
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65909178..65910737-chr11:65912295..65914577,2	MCF-7	breast:
2	chr11:65835157..65840095-chr11:65905234..65913819,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255038	Chromatin interaction
ENSG00000175115	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1055615	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10791853	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10791856	0.88[ASN][1000 genomes]
rs10896092	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896095	0.84[ASN][1000 genomes]
rs10896097	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227426	0.88[ASN][1000 genomes]
rs12049852	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1717671	0.89[ASN][1000 genomes]
rs1987678	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3088328	0.86[ASN][1000 genomes]
rs471484	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs472518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs475805	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs485857	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488320	0.92[ASN][1000 genomes]
rs489337	0.90[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs524281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs527897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs535395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs547087	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs549187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs571434	0.90[ASN][1000 genomes]
rs580891	0.86[ASN][1000 genomes]
rs708471	0.83[AFR][1000 genomes]
rs708472	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs7937281	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7941469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7942894	0.85[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	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs565198	RP11-867O8.5	cis	Artery Aorta	GTEx
rs565198	KLC2	cis	Muscle Skeletal	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65895000-65913800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:65895000-65917600	Weak transcription	HSMM	muscle
3	chr11:65901000-65919400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr11:65905200-65947000	Weak transcription	Fetal Lung	lung
5	chr11:65905400-65939600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr11:65905800-65924200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:65905800-65952800	Weak transcription	Fetal Stomach	stomach
8	chr11:65906000-65960200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:65909800-65914200	Weak transcription	Esophagus	oesophagus
10	chr11:65909800-65914200	Enhancers	HepG2	liver
11	chr11:65910000-65914000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:65910000-65914200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:65910000-65939600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:65910200-65913800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr11:65910400-65913800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr11:65910400-65916000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:65910400-65918600	Weak transcription	HSMMtube	muscle
18	chr11:65910400-65927000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:65910600-65917400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:65910600-65939600	Weak transcription	NHDF-Ad	bronchial
21	chr11:65910800-65917400	Weak transcription	NHLF	lung
22	chr11:65910800-65917600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:65911000-65918800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:65911000-65924400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:65911000-65924400	Weak transcription	NHEK	skin
26	chr11:65911000-65924600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:65911000-65939400	Weak transcription	NH-A	brain
28	chr11:65911000-65943200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:65911800-65914200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:65911800-65916600	Weak transcription	K562	blood
31	chr11:65912200-65914000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:65912200-65914000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr11:65912400-65913600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr11:65912400-65914000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:65912400-65914400	Genic enhancers	Primary T cells from cord blood	blood
36	chr11:65912400-65914600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:65912400-65915200	ZNF genes & repeats	GM12878-XiMat	blood
38	chr11:65912600-65914200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:65912600-65914200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:65912800-65913800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr11:65912800-65917600	Weak transcription	Primary B cells from cord blood	blood
42	chr11:65912800-65924400	Weak transcription	A549	lung
43	chr11:65913000-65918800	Weak transcription	Small Intestine	intestine
44	chr11:65913200-65913600	Enhancers	HUVEC	blood vessel
45	chr11:65913200-65913800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:65913200-65914000	Weak transcription	Aorta	Aorta
47	chr11:65913200-65918400	Weak transcription	Right Atrium	heart
48	chr11:65913200-65918800	Weak transcription	Left Ventricle	heart
49	chr11:65913200-65927000	Weak transcription	Right Ventricle	heart
50	chr11:65913200-65927200	Weak transcription	Duodenum Mucosa	Duodenum

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