Variant report

Variant	rs11577677
Chromosome Location	chr1:221999547-221999548
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11590053	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17010889	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3010850	0.88[EUR][1000 genomes]
rs4418610	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4528124	0.82[JPT][hapmap]
rs4551601	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639769	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61825191	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61825193	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825195	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514382	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515604	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519761	0.82[JPT][hapmap]
rs7544656	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441877	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441974	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441979	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv873201	chr1:221956626-222007535	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221967400-222009800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:221990600-222000200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:221991600-222000400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:221996800-222000400	Weak transcription	Brain Substantia Nigra	brain
5	chr1:221997200-222000400	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:221997600-222000200	Weak transcription	NHLF	lung
7	chr1:221997800-222000000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:221997800-222000400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:221998000-222000200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:221998000-222000200	Weak transcription	A549	lung
11	chr1:221998000-222000400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:221998000-222003000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:221998200-222000000	Weak transcription	NHDF-Ad	bronchial
14	chr1:221998200-222000000	Weak transcription	NHEK	skin
15	chr1:221998200-222000000	Weak transcription	Osteobl	bone
16	chr1:221998400-222000000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:221998400-222000200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:221998400-222000200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:221998400-222000200	Weak transcription	NH-A	brain
20	chr1:221998600-222000000	Weak transcription	GM12878-XiMat	blood
21	chr1:221998600-222000000	Weak transcription	HMEC	breast
22	chr1:221998600-222001200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:221998800-222000800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:221999200-221999800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:221999200-222000000	Weak transcription	Hela-S3	cervix
26	chr1:221999200-222000200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:221999400-221999600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:221999400-222000400	Weak transcription	Pancreas	Pancrea
29	chr1:221999400-222004200	Enhancers	HUVEC	blood vessel

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