Variant report

Variant	rs6860716
Chromosome Location	chr5:179162840-179162841
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179123632..179128657-chr5:179156913..179163491,14	MCF-7	breast:
2	chr5:179161523..179163573-chr5:179243732..179245347,2	MCF-7	breast:
3	chr5:179122873..179128898-chr5:179155888..179164921,20	K562	blood:
4	chr5:179157089..179164271-chr5:179242384..179250347,16	K562	blood:
5	chr5:179158557..179162046-chr5:179162635..179164608,3	K562	blood:
6	chr5:179161775..179164271-chr5:179248764..179250347,2	K562	blood:
7	chr5:179161374..179164232-chr5:179220024..179222829,2	MCF-7	breast:
8	chr5:179143486..179153989-chr5:179156108..179164461,19	MCF-7	breast:
9	chr5:179157523..179162988-chr5:179219694..179224698,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000127022	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000213316	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11738269	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11738720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11739042	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11740569	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11741570	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11743232	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11744616	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11746924	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11747496	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12522263	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469020	0.90[ASN][1000 genomes]
rs1469021	0.90[ASN][1000 genomes]
rs17617068	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17617710	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34057110	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3756614	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3797762	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797776	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41458244	0.90[ASN][1000 genomes]
rs4700838	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700840	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55654737	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55827522	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55975622	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56309143	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56335144	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58386410	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62404347	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406176	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62406177	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62406178	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62406181	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62406187	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406219	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62406223	0.87[ASN][1000 genomes]
rs6601067	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6601072	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6887507	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6893300	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6895902	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs730012	0.90[ASN][1000 genomes]
rs7444006	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7447159	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7704520	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7705530	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7709723	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7715356	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7734102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7735702	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 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	chr5:179161000-179163200	Enhancers	Primary B cells from peripheral blood	blood
2	chr5:179161000-179163600	Enhancers	Small Intestine	intestine
3	chr5:179161000-179164600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:179161000-179174000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:179161000-179174000	Weak transcription	Gastric	stomach
6	chr5:179161000-179174200	Weak transcription	Esophagus	oesophagus
7	chr5:179161000-179181200	Weak transcription	Aorta	Aorta
8	chr5:179161000-179181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:179161000-179181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:179161200-179166000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr5:179161400-179165600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr5:179161600-179163000	Enhancers	Spleen	Spleen
13	chr5:179161600-179163200	Enhancers	Adipose Nuclei	Adipose
14	chr5:179161600-179163200	Genic enhancers	Fetal Muscle Leg	muscle
15	chr5:179161600-179163400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:179161600-179163400	Genic enhancers	Fetal Thymus	thymus
17	chr5:179161600-179163800	Enhancers	Fetal Brain Male	brain
18	chr5:179161600-179163800	Enhancers	Lung	lung
19	chr5:179161600-179164200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:179161600-179164800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr5:179161600-179165000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:179161600-179165400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:179161600-179176600	Weak transcription	HSMMtube	muscle
24	chr5:179161800-179163000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr5:179161800-179163000	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:179161800-179163200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr5:179161800-179163400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:179161800-179163400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr5:179161800-179164000	Enhancers	HepG2	liver
30	chr5:179161800-179164200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:179161800-179164200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr5:179161800-179164200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:179161800-179164200	Weak transcription	Brain Substantia Nigra	brain
34	chr5:179161800-179164200	Enhancers	Duodenum Mucosa	Duodenum
35	chr5:179161800-179164400	Enhancers	Left Ventricle	heart
36	chr5:179161800-179164800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:179161800-179165600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:179161800-179166000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:179161800-179166400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:179161800-179174200	Weak transcription	A549	lung
41	chr5:179161800-179176600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:179161800-179176800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr5:179161800-179177400	Weak transcription	Fetal Kidney	kidney
44	chr5:179161800-179188800	Weak transcription	NHDF-Ad	bronchial
45	chr5:179162000-179163000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:179162000-179163000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:179162000-179163000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:179162000-179163000	Weak transcription	Right Ventricle	heart
49	chr5:179162000-179163000	Enhancers	Stomach Smooth Muscle	stomach
50	chr5:179162000-179163000	Enhancers	Dnd41	blood

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