Variant report

Variant	rs30407
Chromosome Location	chr16:79624107-79624108
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:79615508..79619075-chr16:79622331..79625028,3	MCF-7	breast:
2	chr16:79622643..79628144-chr16:79628669..79635430,10	MCF-7	breast:
3	chr16:79615551..79617830-chr16:79623732..79625309,2	MCF-7	breast:
4	chr16:79590048..79591563-chr16:79622856..79624638,2	MCF-7	breast:
5	chr16:79620671..79624477-chr16:79631778..79634949,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178573	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs185133	0.84[ASN][1000 genomes]
rs250158	0.84[ASN][1000 genomes]
rs250165	0.84[ASN][1000 genomes]
rs250166	0.84[ASN][1000 genomes]
rs250170	0.84[ASN][1000 genomes]
rs30405	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs30406	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30408	1.00[ASN][1000 genomes]
rs30411	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381823	0.84[ASN][1000 genomes]
rs398465	0.84[ASN][1000 genomes]
rs399239	0.84[ASN][1000 genomes]
rs40965	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193362	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv833295	chr16:79568878-79726768	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv457554	chr16:79608408-79645989	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv573289	chr16:79608408-79645989	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv827768	chr16:79615278-79640094	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79615800-79627200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:79622200-79631400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:79623000-79626800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr16:79623200-79624200	Active TSS	Brain Anterior Caudate	brain
5	chr16:79623200-79624600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr16:79623400-79624200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr16:79623400-79624200	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr16:79623600-79624200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr16:79623600-79624600	Weak transcription	Fetal Lung	lung
10	chr16:79623800-79624200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr16:79623800-79624200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr16:79623800-79624800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr16:79623800-79625800	Enhancers	Brain Substantia Nigra	brain
14	chr16:79623800-79626000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr16:79623800-79629200	Weak transcription	Aorta	Aorta
16	chr16:79624000-79624200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
17	chr16:79624000-79624200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr16:79624000-79624200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr16:79624000-79624200	Bivalent/Poised TSS	Colonic Mucosa	Colon
20	chr16:79624000-79624200	Weak transcription	Fetal Intestine Small	intestine
21	chr16:79624000-79624200	Flanking Active TSS	Ovary	ovary
22	chr16:79624000-79624400	Enhancers	Brain Hippocampus Middle	brain
23	chr16:79624000-79624400	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr16:79624000-79624400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr16:79624000-79624400	Enhancers	Stomach Smooth Muscle	stomach
26	chr16:79624000-79624600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr16:79624000-79624800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr16:79624000-79624800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
29	chr16:79624000-79624800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr16:79624000-79624800	Enhancers	Brain Cingulate Gyrus	brain
31	chr16:79624000-79624800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr16:79624000-79624800	Enhancers	Esophagus	oesophagus
33	chr16:79624000-79625200	Enhancers	Psoas Muscle	Psoas
34	chr16:79624000-79625400	Enhancers	Liver	Liver
35	chr16:79624000-79625800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr16:79624000-79625800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:79624000-79626000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr16:79624000-79626000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr16:79624000-79626000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr16:79624000-79626200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr16:79624000-79626400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr16:79624000-79626400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr16:79624000-79626800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr16:79624000-79626800	Enhancers	Adipose Nuclei	Adipose
45	chr16:79624000-79626800	Weak transcription	Right Atrium	heart
46	chr16:79624000-79627200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr16:79624000-79628800	Weak transcription	Colon Smooth Muscle	Colon
48	chr16:79624000-79629000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr16:79624000-79629800	Weak transcription	Fetal Muscle Trunk	muscle

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