Variant report

Variant	rs17767188
Chromosome Location	chr14:65188240-65188241
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr14:65187965-65188635	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr14:65187902-65188622	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr14:65187875-65188662	ECC-1	luminal epithelium:	n/a	chr14:65188221-65188231
4	TEAD4	chr14:65187983-65188576	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr14:65188005-65188682	ECC-1	luminal epithelium:	n/a	chr14:65188221-65188231
6	USF1	chr14:65188057-65188568	ECC-1	luminal epithelium:	n/a	n/a
7	MYC	chr14:65187971-65188347	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr14:65188147-65188531	NB4	blood:	n/a	n/a
9	EBF1	chr14:65188049-65188772	GM12878	blood:	n/a	chr14:65188371-65188380 chr14:65188479-65188489 chr14:65188369-65188382
10	MAX	chr14:65187995-65188561	ECC-1	luminal epithelium:	n/a	n/a
11	USF1	chr14:65188064-65188507	ECC-1	luminal epithelium:	n/a	n/a
12	ZBTB7A	chr14:65188125-65188721	ECC-1	luminal epithelium:	n/a	n/a
13	NFIC	chr14:65187963-65188693	ECC-1	luminal epithelium:	n/a	n/a
14	EBF1	chr14:65188204-65188429	GM12878	blood:	n/a	chr14:65188371-65188380 chr14:65188369-65188382
15	MAX	chr14:65188034-65188515	NB4	blood:	n/a	n/a
16	MAX	chr14:65187874-65188380	A549	lung:	n/a	n/a
17	TEAD4	chr14:65187921-65188472	ECC-1	luminal epithelium:	n/a	chr14:65187960-65187969
18	BHLHE40	chr14:65188221-65188515	GM12878	blood:	n/a	n/a
19	EP300	chr14:65188041-65188723	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:65005659..65008435-chr14:65184165..65188343,3	MCF-7	breast:
2	chr14:64969647..64971800-chr14:65185515..65189340,6	MCF-7	breast:
3	chr14:65187766..65189272-chr14:65190644..65193046,2	K562	blood:
4	chr14:65005225..65007322-chr14:65187172..65189732,2	MCF-7	breast:
5	chr14:65185854..65191054-chr14:65221241..65225762,8	MCF-7	breast:
6	chr14:65148900..65150464-chr14:65186037..65188877,2	MCF-7	breast:
7	chr14:65182036..65184800-chr14:65187210..65189994,3	MCF-7	breast:
8	chr14:65168529..65178400-chr14:65179583..65195815,52	MCF-7	breast:

No data

Variant related genes	Relation type
PLEKHG3	TF binding region
ENSG00000126822	Chromatin interaction
ENSG00000126803	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000259116	Chromatin interaction
ENSG00000070182	Chromatin interaction
ENSG00000089775	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17179970	0.87[ASN][1000 genomes]
rs17179984	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17180090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767206	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1985466	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1998120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs229624	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs229625	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs229626	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs229644	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs229646	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs229650	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs229651	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs229659	0.92[ASN][1000 genomes]
rs229660	1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs229662	0.91[ASN][1000 genomes]
rs229663	0.91[ASN][1000 genomes]
rs229664	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs41301473	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41307086	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58789159	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73273513	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73273517	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73273524	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73273534	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73273536	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73273546	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73273549	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs754435	0.91[ASN][1000 genomes]
rs872296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049097	chr14:65027753-65202018	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1818582	chr14:65172898-65256685	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1035833	chr14:65176371-65246181	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17767188	PLEKHG3	cis	multi-tissue	Pritchard
rs17767188	PLEKHG3	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65177000-65189200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr14:65181000-65189400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr14:65181000-65197600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr14:65181200-65189600	Enhancers	Liver	Liver
5	chr14:65181200-65197000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr14:65181600-65189400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr14:65181800-65188800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr14:65181800-65190600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr14:65181800-65192400	Enhancers	Adipose Nuclei	Adipose
10	chr14:65181800-65194400	Enhancers	Placenta Amnion	Placenta Amnion
11	chr14:65182000-65190800	Enhancers	Stomach Mucosa	stomach
12	chr14:65182200-65191600	Enhancers	Spleen	Spleen
13	chr14:65182800-65193800	Enhancers	Esophagus	oesophagus
14	chr14:65183000-65194600	Weak transcription	Fetal Brain Female	brain
15	chr14:65183000-65196200	Genic enhancers	Fetal Intestine Small	intestine
16	chr14:65183400-65188400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr14:65183400-65190000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr14:65183400-65194200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr14:65183600-65188800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr14:65183600-65188800	Enhancers	Fetal Lung	lung
21	chr14:65183600-65189600	Enhancers	Ovary	ovary
22	chr14:65183600-65190000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr14:65183600-65190000	Enhancers	Duodenum Mucosa	Duodenum
24	chr14:65183600-65193800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr14:65183800-65191800	Weak transcription	Brain Germinal Matrix	brain
26	chr14:65183800-65193400	Enhancers	Right Atrium	heart
27	chr14:65183800-65193800	Enhancers	Pancreas	Pancrea
28	chr14:65184000-65208800	Weak transcription	Fetal Brain Male	brain
29	chr14:65184200-65188400	Enhancers	H9 Cell Line	embryonic stem cell
30	chr14:65184200-65188400	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr14:65184200-65189200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:65184200-65189600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr14:65184200-65189600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr14:65184200-65193800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr14:65184400-65189200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr14:65184400-65189200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr14:65184600-65188400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:65184600-65188800	Genic enhancers	NHEK	skin
39	chr14:65184600-65189400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr14:65184600-65189400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr14:65184600-65193200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr14:65184800-65188400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr14:65185200-65189600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr14:65185400-65188600	Enhancers	NHLF	lung
45	chr14:65185400-65189200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr14:65185400-65189600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr14:65185400-65190000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr14:65185400-65190000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr14:65185600-65189000	Genic enhancers	Fetal Stomach	stomach
50	chr14:65185800-65193600	Enhancers	Brain Angular Gyrus	brain

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