Variant report

Variant	rs560807
Chromosome Location	chr11:34468639-34468640
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34387533..34389876-chr11:34467874..34469738,2	K562	blood:
2	chr11:34467629..34470088-chr11:34474933..34478324,3	K562	blood:
3	chr11:34463426..34466853-chr11:34467996..34471084,4	K562	blood:
4	chr11:34459310..34462934-chr11:34466311..34470636,5	K562	blood:
5	chr11:34468515..34471124-chr11:34484849..34487654,3	K562	blood:

Variant related genes	Relation type
ENSG00000121691	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1001179	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10836230	0.86[CEU][hapmap]
rs10836234	0.85[CEU][hapmap]
rs11032654	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11032695	0.85[CEU][hapmap]
rs11032718	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032719	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11032722	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032723	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032724	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032726	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11032728	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11604331	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1267468	1.00[YRI][hapmap]
rs12790145	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12797274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12797675	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12807961	0.85[CEU][hapmap]
rs12808450	0.85[CEU][hapmap]
rs1408041	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1535719	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17269903	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17269931	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146962	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2231821	0.90[ASN][1000 genomes]
rs2231825	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2231828	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420386	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2476504	1.00[JPT][hapmap]
rs34234992	0.90[ASN][1000 genomes]
rs34366473	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34901344	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35495760	0.90[ASN][1000 genomes]
rs475043	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756135	1.00[YRI][hapmap]
rs494024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508370	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs511895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55898107	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737254	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][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	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs560807	CAT	cis	Whole Blood	GTEx
rs560807	CAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34461400-34472200	Weak transcription	Aorta	Aorta
2	chr11:34461400-34473200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:34461400-34482800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:34461600-34470200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:34461600-34471400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:34461800-34469800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:34461800-34470200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:34461800-34471400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:34461800-34471400	Weak transcription	Placenta	Placenta
10	chr11:34461800-34471400	Weak transcription	HSMM	muscle
11	chr11:34461800-34471400	Weak transcription	NH-A	brain
12	chr11:34461800-34471400	Weak transcription	NHEK	skin
13	chr11:34461800-34472200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:34461800-34472200	Weak transcription	Esophagus	oesophagus
15	chr11:34461800-34472200	Weak transcription	Lung	lung
16	chr11:34461800-34485800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:34462000-34469200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:34462000-34469400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:34462000-34469400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:34462000-34469800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:34462000-34469800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:34462000-34470600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:34462000-34470800	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:34462000-34470800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr11:34462000-34470800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr11:34462000-34470800	Weak transcription	Osteobl	bone
27	chr11:34462000-34471400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr11:34462000-34471400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:34462000-34471400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr11:34462000-34471400	Weak transcription	HUVEC	blood vessel
31	chr11:34462000-34471400	Weak transcription	NHLF	lung
32	chr11:34462000-34472200	Weak transcription	Fetal Stomach	stomach
33	chr11:34462000-34472200	Weak transcription	Right Ventricle	heart
34	chr11:34462000-34474600	Weak transcription	Fetal Brain Male	brain
35	chr11:34462000-34477600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:34462600-34469200	Weak transcription	Primary T cells from cord blood	blood
37	chr11:34462600-34471000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr11:34462600-34471400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:34462800-34469200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr11:34463000-34469200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr11:34463200-34469400	Weak transcription	Fetal Intestine Large	intestine
42	chr11:34463200-34469600	Enhancers	Primary hematopoietic stem cells	blood
43	chr11:34463400-34469200	Weak transcription	Thymus	Thymus
44	chr11:34463400-34469400	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr11:34463400-34469400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr11:34463400-34469400	Weak transcription	Pancreas	Pancrea
47	chr11:34463400-34471400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:34463400-34473600	Weak transcription	Fetal Intestine Small	intestine
49	chr11:34463600-34469200	Weak transcription	Fetal Muscle Leg	muscle
50	chr11:34463600-34469800	Weak transcription	Hela-S3	cervix

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