Variant report

Variant	rs29001609
Chromosome Location	chr1:171160955-171160956
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	chr1:171151483..171154581-chr1:171157949..171161924,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000094963	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10912525	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12064117	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12066662	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12067810	0.81[EUR][1000 genomes]
rs12071595	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12072321	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12072579	0.83[AFR][1000 genomes]
rs12076944	0.83[AFR][1000 genomes]
rs12078869	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12079736	0.83[AFR][1000 genomes]
rs12082112	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12082366	0.83[AFR][1000 genomes]
rs12086788	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12087971	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12091865	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16864136	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16864165	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16864191	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2020860	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2020865	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2205726	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2421708	0.88[AFR][1000 genomes]
rs28369791	0.88[AFR][1000 genomes]
rs28369796	0.88[AFR][1000 genomes]
rs28369826	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28369834	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28369837	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28369850	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28369868	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28369872	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28369883	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28369886	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28969551	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56060753	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56159716	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56233063	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57182460	0.81[EUR][1000 genomes]
rs58324390	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58956470	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59910498	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61225278	0.84[EUR][1000 genomes]
rs6668231	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6673781	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6689616	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73032526	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74122287	0.84[AMR][1000 genomes];0.84[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	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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171156400-171165800	Weak transcription	Gastric	stomach
2	chr1:171156600-171163800	Weak transcription	Small Intestine	intestine
3	chr1:171156600-171169800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:171156600-171177200	Weak transcription	Esophagus	oesophagus
5	chr1:171156600-171179600	Weak transcription	NHLF	lung
6	chr1:171156800-171179600	Weak transcription	Right Ventricle	heart
7	chr1:171157800-171165600	Weak transcription	Ovary	ovary
8	chr1:171158200-171167000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:171158400-171161000	Enhancers	Stomach Mucosa	stomach
10	chr1:171158400-171165600	Weak transcription	Fetal Lung	lung
11	chr1:171159000-171162000	Enhancers	Adipose Nuclei	Adipose
12	chr1:171159000-171165800	Weak transcription	Lung	lung
13	chr1:171159800-171161200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:171160000-171164800	Weak transcription	Fetal Intestine Small	intestine
15	chr1:171160000-171165000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:171160200-171166800	Weak transcription	Fetal Brain Male	brain
17	chr1:171160400-171161800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:171160600-171163600	Weak transcription	Fetal Intestine Large	intestine
19	chr1:171160800-171161000	Enhancers	Aorta	Aorta
20	chr1:171160800-171161000	Flanking Active TSS	Right Atrium	heart
21	chr1:171160800-171161200	Enhancers	Left Ventricle	heart
22	chr1:171160800-171161200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:171160800-171161800	Enhancers	Liver	Liver

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