Variant report

Variant	rs6684218
Chromosome Location	chr1:171220108-171220109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171219827..171222241-chr1:171222983..171225833,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206692	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10912525	0.82[EUR][1000 genomes]
rs12064117	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12066662	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12067810	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12071595	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12072321	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12082112	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12087971	0.82[EUR][1000 genomes]
rs12091865	0.82[EUR][1000 genomes]
rs13353034	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16864165	0.82[EUR][1000 genomes]
rs16864191	0.85[EUR][1000 genomes]
rs16864245	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2020860	0.82[EUR][1000 genomes]
rs2020865	0.85[EUR][1000 genomes]
rs2205726	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28369826	0.82[EUR][1000 genomes]
rs28369834	0.82[EUR][1000 genomes]
rs28369837	0.82[EUR][1000 genomes]
rs28369850	0.82[EUR][1000 genomes]
rs28369883	0.82[EUR][1000 genomes]
rs28369886	0.82[EUR][1000 genomes]
rs28969551	0.82[EUR][1000 genomes]
rs56060753	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56159716	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56233063	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57182460	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58324390	0.85[EUR][1000 genomes]
rs58956470	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59910498	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61225278	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61233777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6668231	0.82[EUR][1000 genomes]
rs6673781	0.82[EUR][1000 genomes]
rs6689616	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73032526	0.82[EUR][1000 genomes]
rs74122287	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7527107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171200800-171220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:171215800-171220200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:171217000-171220200	Weak transcription	Pancreas	Pancrea
4	chr1:171217200-171220400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:171217200-171220400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:171217600-171220200	Weak transcription	Liver	Liver
7	chr1:171217600-171221000	Active TSS	Fetal Intestine Small	intestine
8	chr1:171217600-171221200	Active TSS	Fetal Intestine Large	intestine
9	chr1:171218400-171220200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:171219000-171220200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:171219000-171220200	Weak transcription	NHEK	skin
12	chr1:171219000-171220400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:171219400-171220200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
14	chr1:171219600-171221200	Active TSS	Fetal Lung	lung
15	chr1:171219800-171220200	Enhancers	Primary B cells from cord blood	blood
16	chr1:171219800-171220600	Bivalent/Poised TSS	Fetal Kidney	kidney
17	chr1:171220000-171220200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:171220000-171220200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:171220000-171220400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:171220000-171220400	Bivalent Enhancer	HepG2	liver
21	chr1:171220000-171220800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr1:171220000-171221200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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