Variant report

Variant	rs231016
Chromosome Location	chr17:15166985-15166986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr17:15165603-15167148	A549	lung:	n/a	chr17:15166695-15166704 chr17:15166649-15166658
2	POLR2A	chr17:15163626-15167137	IMR90	lung:	n/a	n/a
3	RAD21	chr17:15163681-15167318	IMR90	lung:	n/a	chr17:15165861-15165873 chr17:15166929-15166941
4	BCL3	chr17:15164294-15167367	A549	lung:	n/a	chr17:15166341-15166354 chr17:15165839-15165852 chr17:15165814-15165827 chr17:15165831-15165844 chr17:15165654-15165667
5	E2F6	chr17:15165234-15166993	A549	lung:	n/a	chr17:15166247-15166256 chr17:15165823-15165830 chr17:15166646-15166653 chr17:15165349-15165358 chr17:15166645-15166656 chr17:15165816-15165826 chr17:15166646-15166654 chr17:15166645-15166655 chr17:15165658-15165667 chr17:15166646-15166654 chr17:15165850-15165861 chr17:15166646-15166657
6	ZNF143	chr17:15166419-15167369	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr17:15163434-15167583	SK-N-SH	brain:	n/a	chr17:15165861-15165873 chr17:15166929-15166941
8	NFIC	chr17:15163497-15167079	SK-N-SH	brain:	n/a	chr17:15166620-15166637 chr17:15166620-15166636 chr17:15166607-15166623
9	POLR2A	chr17:15165256-15167006	U87	brain:	n/a	n/a
10	EP300	chr17:15166383-15167034	A549	lung:	n/a	chr17:15166941-15166948
11	POLR2A	chr17:15165399-15167043	U87	brain:	n/a	n/a
12	SP1	chr17:15165159-15167451	A549	lung:	n/a	chr17:15165200-15165213 chr17:15165368-15165382
13	BHLHE40	chr17:15166637-15166995	A549	lung:	n/a	n/a
14	POLR2A	chr17:15165497-15166997	HUVEC	blood vessel:	n/a	n/a
15	RAD21	chr17:15166428-15167298	H1-hESC	embryonic stem cell:	n/a	chr17:15166929-15166941
16	CTCF	chr17:15163357-15167631	A549	lung:	n/a	chr17:15166140-15166147 chr17:15164224-15164237 chr17:15164251-15164264
17	MAZ	chr17:15163312-15167057	IMR90	lung:	n/a	chr17:15164861-15164870 chr17:15164860-15164870 chr17:15164862-15164869 chr17:15164860-15164871
18	MAX	chr17:15165638-15166992	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr17:15165420-15167037	U87	brain:	n/a	n/a
20	MAX	chr17:15165328-15167013	SK-N-SH	brain:	n/a	n/a
21	MAX	chr17:15163483-15167382	A549	lung:	n/a	chr17:15164861-15164870 chr17:15164860-15164870 chr17:15164862-15164869 chr17:15164860-15164871
22	GATA3	chr17:15165510-15167308	A549	lung:	n/a	chr17:15167100-15167107 chr17:15166606-15166614 chr17:15167093-15167109
23	BACH1	chr17:15166652-15167018	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr17:15163586-15167452	SK-N-SH	brain:	n/a	chr17:15166140-15166147 chr17:15164224-15164237 chr17:15164251-15164264
25	SP1	chr17:15165468-15167057	A549	lung:	n/a	n/a
26	TCF12	chr17:15163428-15167498	A549	lung:	n/a	chr17:15164244-15164254
27	MAX	chr17:15166527-15167017	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr17:15165193-15167149	A549	lung:	n/a	n/a
29	REST	chr17:15165012-15167082	A549	lung:	n/a	chr17:15167003-15167011 chr17:15165636-15165646 chr17:15165831-15165844
30	SMC3	chr17:15163313-15167426	SK-N-SH	brain:	n/a	chr17:15164224-15164234 chr17:15166295-15166305
31	SIN3A	chr17:15165489-15167066	H1-hESC	embryonic stem cell:	n/a	n/a
32	NRF1	chr17:15165427-15167573	SK-N-SH	brain:	n/a	chr17:15165843-15165857 chr17:15165657-15165668 chr17:15166245-15166259 chr17:15165845-15165856 chr17:15165657-15165671 chr17:15165654-15165668 chr17:15166248-15166262 chr17:15166247-15166256

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15166284..15168477-chr17:15174435..15176206,2	MCF-7	breast:
2	chr17:15166025..15168279-chr17:15170899..15173519,3	MCF-7	breast:

Variant related genes	Relation type
PMP22	TF binding region
ENSG00000230971	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs230911	0.84[ASN][1000 genomes]
rs231014	0.94[ASN][1000 genomes]
rs231015	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs231017	0.89[EUR][1000 genomes]
rs231019	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs231022	0.88[ASN][1000 genomes]
rs231024	0.87[ASN][1000 genomes]
rs55568	0.83[EUR][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	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15162400-15167000	Active TSS	Psoas Muscle	Psoas
2	chr17:15163000-15167000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr17:15163000-15167000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr17:15163000-15167000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr17:15163000-15167000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:15163200-15168400	Active TSS	Right Atrium	heart
7	chr17:15163400-15167000	Active TSS	Ovary	ovary
8	chr17:15163400-15167000	Flanking Active TSS	HMEC	breast
9	chr17:15163400-15167200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr17:15163400-15168000	Active TSS	Left Ventricle	heart
11	chr17:15163600-15167000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr17:15163600-15167000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr17:15163600-15167000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr17:15163600-15167000	Active TSS	Colon Smooth Muscle	Colon
15	chr17:15163600-15167200	Active TSS	Brain Anterior Caudate	brain
16	chr17:15163800-15167200	Active TSS	Brain Substantia Nigra	brain
17	chr17:15164000-15167000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:15164000-15167000	Active TSS	Brain Angular Gyrus	brain
19	chr17:15164400-15167000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr17:15164400-15167000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:15164400-15167000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
22	chr17:15164400-15167000	Flanking Active TSS	NH-A	brain
23	chr17:15164800-15167000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:15164800-15167000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
25	chr17:15164800-15167200	Bivalent/Poised TSS	Fetal Kidney	kidney
26	chr17:15165000-15167000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
27	chr17:15165000-15167000	Active TSS	Rectal Smooth Muscle	rectum
28	chr17:15165200-15167000	Flanking Bivalent TSS/Enh	NHEK	skin
29	chr17:15165200-15167400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr17:15165400-15167000	Flanking Active TSS	Pancreas	Pancrea
31	chr17:15165600-15167000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr17:15165600-15167000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr17:15165600-15167000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:15165800-15167000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr17:15165800-15167000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:15165800-15167000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:15165800-15167600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr17:15166000-15167000	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr17:15166000-15167200	Flanking Active TSS	NHLF	lung
40	chr17:15166000-15167600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr17:15166200-15167000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr17:15166200-15167000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:15166200-15167000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
44	chr17:15166200-15167000	Flanking Active TSS	Osteobl	bone
45	chr17:15166200-15167200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr17:15166200-15167200	Bivalent Enhancer	Fetal Brain Male	brain
47	chr17:15166200-15167400	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr17:15166400-15167000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr17:15166400-15167000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:15166400-15167000	Active TSS	Adipose Nuclei	Adipose

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