Variant report

Variant	rs16835339
Chromosome Location	chr1:153459396-153459397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153323483..153340048-chr1:153448254..153469845,61	MCF-7	breast:
2	chr1:153367009..153368544-chr1:153456624..153459819,3	MCF-7	breast:
3	chr1:153457718..153462195-chr1:153468437..153470953,3	K562	blood:
4	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
5	chr1:153455880..153459414-chr1:153459858..153461522,3	MCF-7	breast:
6	chr1:153459205..153462195-chr1:153468437..153470623,2	K562	blood:

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction
ENSG00000163218	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11205297	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12021612	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022550	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024114	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12025638	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044034	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12047203	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12047494	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16835332	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339695	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28696717	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2986209	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014848	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55703007	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56009204	0.89[ASN][1000 genomes]
rs72708789	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
6	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153451000-153467400	Weak transcription	Ovary	ovary
2	chr1:153455400-153462200	Weak transcription	Right Ventricle	heart
3	chr1:153456800-153461400	Weak transcription	Hela-S3	cervix
4	chr1:153457200-153460200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:153457200-153461000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:153457200-153462600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:153457200-153465800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:153457600-153459400	Enhancers	Fetal Heart	heart
9	chr1:153458200-153461200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:153458400-153461000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:153458800-153461200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:153459000-153460400	Weak transcription	HMEC	breast
13	chr1:153459000-153461000	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:153459000-153461200	Weak transcription	Left Ventricle	heart
15	chr1:153459000-153461200	Weak transcription	Right Atrium	heart
16	chr1:153459000-153461400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:153459000-153461400	Weak transcription	Esophagus	oesophagus
18	chr1:153459000-153461400	Weak transcription	NHEK	skin
19	chr1:153459000-153467800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:153459200-153462600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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