Variant report

Variant	rs499733
Chromosome Location	chr22:27600604-27600605
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:27066818..27069274-chr22:27599174..27601990,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRYBA4-6	chr22:27596085-27601088	NONHSAT084576

Variant related genes	Relation type
ENSG00000206028	Chromatin interaction
ENSG00000244625	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1401522	0.89[EUR][1000 genomes]
rs491735	0.90[ASN][1000 genomes]
rs492416	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs494604	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs497365	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs497368	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs499712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500281	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs530536	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs555860	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs561417	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs849449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs864754	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9613395	0.95[CEU][hapmap]

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	nsv917333	chr22:26931825-27692024	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	142 gene(s)	inside rSNPs	diseases
2	esv34168	chr22:27289097-27678031	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27593600-27608800	Weak transcription	Right Atrium	heart
2	chr22:27598400-27607800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr22:27598800-27601400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:27599200-27601600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr22:27599200-27602200	Weak transcription	Aorta	Aorta
6	chr22:27599200-27602200	Weak transcription	Colon Smooth Muscle	Colon
7	chr22:27599400-27603600	Weak transcription	Adipose Nuclei	Adipose
8	chr22:27599400-27603800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:27599600-27601400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr22:27599600-27601600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:27599600-27601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr22:27599600-27601800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr22:27599600-27601800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr22:27599600-27601800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr22:27599600-27601800	Weak transcription	HSMM	muscle
16	chr22:27599600-27602200	Weak transcription	HSMMtube	muscle
17	chr22:27599600-27602400	Weak transcription	Fetal Brain Female	brain
18	chr22:27599600-27608600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr22:27599800-27601800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr22:27599800-27601800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:27599800-27601800	Weak transcription	NH-A	brain
22	chr22:27599800-27601800	Weak transcription	Osteobl	bone
23	chr22:27599800-27602200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr22:27599800-27602400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr22:27599800-27603800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr22:27599800-27606200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr22:27600000-27600800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr22:27600000-27601200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr22:27600000-27601400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr22:27600000-27601400	Weak transcription	Fetal Stomach	stomach
31	chr22:27600000-27601600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr22:27600000-27601600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr22:27600000-27601800	Weak transcription	NHEK	skin
34	chr22:27600000-27602200	Weak transcription	A549	lung
35	chr22:27600400-27601600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr22:27600400-27601600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr22:27600400-27601600	Weak transcription	Esophagus	oesophagus
38	chr22:27600400-27603600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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