Variant report

Variant	rs16835341
Chromosome Location	chr1:153461298-153461299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153445167..153447773-chr1:153461159..153464090,2	MCF-7	breast:
2	chr1:153460521..153462645-chr1:153469945..153471871,2	MCF-7	breast:
3	chr1:153323483..153340048-chr1:153448254..153469845,61	MCF-7	breast:
4	chr1:153457718..153462195-chr1:153468437..153470953,3	K562	blood:
5	chr1:153452726..153455263-chr1:153460858..153463511,2	MCF-7	breast:
6	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
7	chr1:153354527..153358677-chr1:153460629..153464225,4	MCF-7	breast:
8	chr1:153455880..153459414-chr1:153459858..153461522,3	MCF-7	breast:
9	chr1:153459205..153462195-chr1:153468437..153470623,2	K562	blood:
10	chr1:153449114..153453479-chr1:153459428..153463150,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction
ENSG00000163218	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1359627	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1409367	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1409368	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1555886	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16835343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1853956	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1998844	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2026563	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339694	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2986206	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2986210	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2986214	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006426	0.84[ASN][1000 genomes]
rs3006428	0.84[ASN][1000 genomes]
rs3006429	0.84[ASN][1000 genomes]
rs3006430	0.82[ASN][1000 genomes]
rs3006433	0.89[ASN][1000 genomes]
rs3006438	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3014829	0.81[ASN][1000 genomes]
rs3014831	0.84[ASN][1000 genomes]
rs3014832	0.83[ASN][1000 genomes]
rs3014833	0.82[ASN][1000 genomes]
rs3014835	0.85[ASN][1000 genomes]
rs3014836	0.89[ASN][1000 genomes]
rs3014838	0.89[ASN][1000 genomes]
rs3014839	0.89[ASN][1000 genomes]
rs3014843	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3014845	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3014849	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014851	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3125233	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667320	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs719081	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs875501	0.85[ASN][1000 genomes]
rs9435988	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9633411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:40 , 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	chr1:153457200-153462600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:153457200-153465800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:153459000-153461400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:153459000-153461400	Weak transcription	Esophagus	oesophagus
8	chr1:153459000-153461400	Weak transcription	NHEK	skin
9	chr1:153459000-153467800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:153459200-153462600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:153460200-153461800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:153460400-153462600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:153460400-153463000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr1:153460600-153464400	Enhancers	Fetal Heart	heart
15	chr1:153461000-153461400	Enhancers	Stomach Smooth Muscle	stomach
16	chr1:153461000-153461600	Enhancers	Colon Smooth Muscle	Colon
17	chr1:153461000-153461600	Enhancers	HSMM	muscle
18	chr1:153461000-153463000	Enhancers	HMEC	breast
19	chr1:153461000-153464400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:153461000-153465000	Enhancers	Fetal Muscle Leg	muscle
21	chr1:153461200-153461400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:153461200-153461400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
23	chr1:153461200-153461400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:153461200-153461600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:153461200-153461600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:153461200-153461600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr1:153461200-153461600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr1:153461200-153461600	Enhancers	Pancreas	Pancrea
29	chr1:153461200-153461600	Enhancers	Psoas Muscle	Psoas
30	chr1:153461200-153461600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr1:153461200-153461600	Enhancers	Osteobl	bone
32	chr1:153461200-153461800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:153461200-153462400	Weak transcription	NHLF	lung
34	chr1:153461200-153462600	Weak transcription	Stomach Mucosa	stomach
35	chr1:153461200-153462800	Enhancers	Left Ventricle	heart
36	chr1:153461200-153462800	Enhancers	Right Atrium	heart
37	chr1:153461200-153463400	Enhancers	Fetal Brain Male	brain
38	chr1:153461200-153464000	Enhancers	Lung	lung
39	chr1:153461200-153464400	Enhancers	Fetal Muscle Trunk	muscle
40	chr1:153461200-153464400	Enhancers	Rectal Smooth Muscle	rectum

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