Variant report

Variant	rs6871454
Chromosome Location	chr5:179764270-179764271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179763941..179765836-chr5:179767390..179770088,2	K562	blood:
2	chr5:179762875..179766753-chr5:179777618..179780359,3	MCF-7	breast:
3	chr5:179761126..179762815-chr5:179764028..179766885,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131459	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1078646	0.88[ASN][1000 genomes]
rs1559114	0.89[ASN][1000 genomes]
rs17080196	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17080199	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303012	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4235511	0.86[ASN][1000 genomes]
rs4566752	0.89[ASN][1000 genomes]
rs4700736	0.86[ASN][1000 genomes]
rs4700943	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62404950	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62404953	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62404956	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62404958	0.86[ASN][1000 genomes]
rs62404959	0.88[ASN][1000 genomes]
rs62406364	0.82[ASN][1000 genomes]
rs6601110	0.99[ASN][1000 genomes]
rs6859159	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6864729	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6870028	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874176	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6884276	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6899097	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72811045	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72811049	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9686940	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
6	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
10	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
11	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv883291	chr5:179755559-179818868	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv984575	chr5:179759624-179791220	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179744000-179766600	Weak transcription	Gastric	stomach
2	chr5:179757000-179779000	Weak transcription	Esophagus	oesophagus
3	chr5:179757800-179765600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:179759000-179764600	Weak transcription	Left Ventricle	heart
5	chr5:179759000-179766600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:179759000-179770200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:179759200-179767800	Weak transcription	Fetal Intestine Small	intestine
8	chr5:179759600-179766600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr5:179759800-179766000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:179759800-179767200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:179760000-179765600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:179760000-179765800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:179760200-179765400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:179760400-179765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:179760400-179765800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:179760400-179767000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:179760600-179764800	Strong transcription	Brain Anterior Caudate	brain
18	chr5:179760600-179765000	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr5:179760600-179765400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:179760600-179765600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:179760600-179765800	Strong transcription	Fetal Muscle Leg	muscle
22	chr5:179760600-179766000	Strong transcription	Fetal Stomach	stomach
23	chr5:179760600-179767000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:179760800-179764800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr5:179760800-179765200	Strong transcription	Ovary	ovary
26	chr5:179760800-179765400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr5:179760800-179765600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:179761000-179765000	Strong transcription	Fetal Brain Female	brain
29	chr5:179761000-179765800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:179761200-179765000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:179761200-179766600	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr5:179761600-179764800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:179761600-179765000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:179761600-179765800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:179761600-179766000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:179761600-179766000	Strong transcription	NH-A	brain
37	chr5:179761600-179766600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:179761600-179770000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:179761600-179770200	Weak transcription	Right Ventricle	heart
40	chr5:179761800-179764400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr5:179761800-179764800	Strong transcription	Osteobl	bone
42	chr5:179761800-179770400	Weak transcription	Colon Smooth Muscle	Colon
43	chr5:179762000-179764600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:179762000-179766600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr5:179762200-179764400	Strong transcription	HSMM	muscle
46	chr5:179762200-179764600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:179762200-179765000	Strong transcription	Adipose Nuclei	Adipose
48	chr5:179762200-179770400	Weak transcription	Hela-S3	cervix
49	chr5:179762400-179765000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:179762600-179764600	Strong transcription	HSMMtube	muscle

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