Variant report

Variant	rs6872162
Chromosome Location	chr5:179995397-179995398
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179975334..179978058-chr5:179994170..179996114,2	MCF-7	breast:
2	chr5:179991328..179993518-chr5:179994470..179996881,2	K562	blood:
3	chr5:179921441..179923328-chr5:179994530..179996709,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113300	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10059433	1.00[AMR][1000 genomes]
rs10072835	1.00[AMR][1000 genomes]
rs10077152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13357229	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17080355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28522110	1.00[AMR][1000 genomes]
rs6880907	0.87[AFR][1000 genomes]
rs6883791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7723088	1.00[AMR][1000 genomes]
rs9329113	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	esv1810959	chr5:179945112-179997861	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179950600-180004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:179960000-180000600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:179960200-179998200	Weak transcription	Spleen	Spleen
4	chr5:179970800-180006600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:179973800-180005200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:179974400-180005800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:179975000-180005800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:179975600-180004600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:179976200-179998200	Weak transcription	Fetal Heart	heart
10	chr5:179976200-180007200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:179978400-179998400	Weak transcription	Aorta	Aorta
12	chr5:179985000-180005600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:179985400-180005800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:179987200-180005800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:179987400-180006000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:179987600-180001400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:179987600-180005600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:179987800-180005200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:179988000-180005600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr5:179988400-179998600	Strong transcription	Primary hematopoietic stem cells	blood
21	chr5:179988400-180005400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:179988400-180005800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:179988400-180005800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:179988400-180005800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:179988600-180004600	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr5:179988600-180005200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:179988800-180005400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:179988800-180005800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:179989000-179997000	Weak transcription	Pancreas	Pancrea
30	chr5:179989000-180002400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:179989400-179999400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:179989800-179997000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:179990600-180004600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:179990600-180005600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:179990800-179995400	Strong transcription	HSMMtube	muscle
36	chr5:179990800-180005400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr5:179991000-179999000	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:179991000-179999000	Strong transcription	Adipose Nuclei	Adipose
39	chr5:179991000-180002000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:179991000-180003600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr5:179991000-180005400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:179991000-180005800	Strong transcription	Primary B cells from cord blood	blood
43	chr5:179991000-180005800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr5:179991000-180005800	Strong transcription	Fetal Intestine Large	intestine
45	chr5:179991000-180006400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:179991200-179996800	Strong transcription	HepG2	liver
47	chr5:179991200-179997000	Strong transcription	NH-A	brain
48	chr5:179991200-180003200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:179991200-180003800	Strong transcription	Primary T cells from cord blood	blood
50	chr5:179991200-180005000	Weak transcription	Brain Cingulate Gyrus	brain

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