Variant report

Variant	rs6689616
Chromosome Location	chr1:171219803-171219804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10912525	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12064117	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066662	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12067810	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12071595	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12072321	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12078869	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12082112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12086788	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12087971	1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12091865	1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13353034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16864136	0.85[EUR][1000 genomes]
rs16864165	1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16864191	1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16864245	0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17350523	0.85[YRI][hapmap]
rs2020860	1.00[GIH][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2020865	1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2075991	0.83[YRI][hapmap]
rs2205726	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28369826	0.90[EUR][1000 genomes]
rs28369834	0.90[EUR][1000 genomes]
rs28369837	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28369850	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28369868	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28369872	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28369883	0.90[EUR][1000 genomes]
rs28369886	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28969551	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs29001609	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56060753	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56159716	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56233063	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57182460	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58324390	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58956470	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59910498	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61225278	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61233777	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6668231	0.91[EUR][1000 genomes]
rs6673781	0.91[EUR][1000 genomes]
rs6684218	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73032526	0.91[EUR][1000 genomes]
rs74122287	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7527107	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[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:18 , 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	chr1:171216000-171220000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:171217000-171220200	Weak transcription	Pancreas	Pancrea
5	chr1:171217200-171220400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:171217200-171220400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:171217600-171220200	Weak transcription	Liver	Liver
8	chr1:171217600-171221000	Active TSS	Fetal Intestine Small	intestine
9	chr1:171217600-171221200	Active TSS	Fetal Intestine Large	intestine
10	chr1:171218400-171220200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:171219000-171220200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:171219000-171220200	Weak transcription	NHEK	skin
13	chr1:171219000-171220400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:171219400-171220200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
15	chr1:171219600-171221200	Active TSS	Fetal Lung	lung
16	chr1:171219800-171220000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr1:171219800-171220200	Enhancers	Primary B cells from cord blood	blood
18	chr1:171219800-171220600	Bivalent/Poised TSS	Fetal Kidney	kidney

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