Variant report

Variant	rs30406
Chromosome Location	chr16:79623085-79623086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:79616352..79617901-chr16:79621545..79623120,2	K562	blood:
2	chr16:79615508..79619075-chr16:79622331..79625028,3	MCF-7	breast:
3	chr16:79622643..79628144-chr16:79628669..79635430,10	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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30407	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30408	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs30411	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[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	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193362	0.88[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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79614600-79623200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr16:79615400-79623200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr16:79615800-79627200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:79620200-79623800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr16:79621600-79623200	Enhancers	Liver	Liver
6	chr16:79622200-79623400	Weak transcription	Right Ventricle	heart
7	chr16:79622200-79631400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:79622600-79623200	Weak transcription	Psoas Muscle	Psoas
9	chr16:79622800-79623200	Bivalent Enhancer	Fetal Kidney	kidney
10	chr16:79623000-79623200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
11	chr16:79623000-79623200	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr16:79623000-79623200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr16:79623000-79623200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr16:79623000-79623200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:79623000-79623200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr16:79623000-79623200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr16:79623000-79623200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr16:79623000-79623200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:79623000-79623200	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
20	chr16:79623000-79623200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
21	chr16:79623000-79623200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr16:79623000-79623200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
23	chr16:79623000-79623200	Bivalent Enhancer	Fetal Intestine Small	intestine
24	chr16:79623000-79623200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr16:79623000-79623400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
26	chr16:79623000-79623400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr16:79623000-79623400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr16:79623000-79623400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
29	chr16:79623000-79623400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
30	chr16:79623000-79623400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
31	chr16:79623000-79623400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr16:79623000-79623400	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr16:79623000-79623400	Enhancers	Brain Substantia Nigra	brain
34	chr16:79623000-79623400	Enhancers	Colon Smooth Muscle	Colon
35	chr16:79623000-79623400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr16:79623000-79623600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr16:79623000-79623600	Active TSS	Fetal Lung	lung
38	chr16:79623000-79623600	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr16:79623000-79623800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
40	chr16:79623000-79623800	Active TSS	Right Atrium	heart
41	chr16:79623000-79623800	Active TSS	Stomach Smooth Muscle	stomach
42	chr16:79623000-79624000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr16:79623000-79624000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr16:79623000-79624000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr16:79623000-79624000	Active TSS	Brain Cingulate Gyrus	brain
46	chr16:79623000-79624000	Active TSS	Brain Hippocampus Middle	brain
47	chr16:79623000-79624000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
48	chr16:79623000-79624000	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr16:79623000-79624000	Active TSS	Ovary	ovary
50	chr16:79623000-79624000	Active TSS	Rectal Smooth Muscle	rectum

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