Variant report

Variant	rs17180090
Chromosome Location	chr14:65190913-65190914
allele	C/T
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	KAP1	chr14:65190823-65191877	U2OS	brain:	n/a	chr14:65191161-65191169
2	ZNF263	chr14:65190564-65191575	HEK293-T-REx	kidney:	n/a	n/a
3	NFIC	chr14:65190756-65191391	ECC-1	luminal epithelium:	n/a	chr14:65191084-65191100
4	KAP1	chr14:65190595-65191842	HEK293	kidney:	n/a	chr14:65191161-65191169

No.	Distal block	Cell Line	Cell type
1	chr14:65185854..65191054-chr14:65221241..65225762,8	MCF-7	breast:
2	chr14:65187766..65189272-chr14:65190644..65193046,2	K562	blood:
3	chr14:65168529..65178400-chr14:65179583..65195815,52	MCF-7	breast:
4	chr14:64969164..64972149-chr14:65189834..65193113,3	MCF-7	breast:

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

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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]
rs17767188	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[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];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1985466	0.96[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];1.00[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	0.82[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	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73273513	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73273517	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73273524	0.82[AMR][1000 genomes];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	0.80[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

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65181000-65197600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr14:65181200-65197000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr14:65181800-65192400	Enhancers	Adipose Nuclei	Adipose
4	chr14:65181800-65194400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr14:65182200-65191600	Enhancers	Spleen	Spleen
6	chr14:65182800-65193800	Enhancers	Esophagus	oesophagus
7	chr14:65183000-65194600	Weak transcription	Fetal Brain Female	brain
8	chr14:65183000-65196200	Genic enhancers	Fetal Intestine Small	intestine
9	chr14:65183400-65194200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr14:65183600-65193800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr14:65183800-65191800	Weak transcription	Brain Germinal Matrix	brain
12	chr14:65183800-65193400	Enhancers	Right Atrium	heart
13	chr14:65183800-65193800	Enhancers	Pancreas	Pancrea
14	chr14:65184000-65208800	Weak transcription	Fetal Brain Male	brain
15	chr14:65184200-65193800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr14:65184600-65193200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr14:65185800-65193600	Enhancers	Brain Angular Gyrus	brain
18	chr14:65186200-65192400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr14:65186400-65191000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr14:65186400-65192400	Enhancers	Osteobl	bone
21	chr14:65186400-65194400	Enhancers	Fetal Intestine Large	intestine
22	chr14:65186600-65191200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr14:65186800-65191000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr14:65186800-65194200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr14:65187000-65192600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr14:65187000-65197400	Enhancers	Primary T cells from cord blood	blood
27	chr14:65187200-65193400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr14:65187400-65195200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr14:65187600-65193200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr14:65187600-65194000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:65188000-65192400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr14:65188000-65192800	Enhancers	Fetal Muscle Trunk	muscle
33	chr14:65188200-65191200	Enhancers	NH-A	brain
34	chr14:65188200-65191600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:65188200-65192800	Weak transcription	HUVEC	blood vessel
36	chr14:65188200-65194000	Enhancers	Colonic Mucosa	Colon
37	chr14:65188400-65191000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr14:65188400-65193200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr14:65188600-65193200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr14:65188600-65193200	Weak transcription	HSMM	muscle
41	chr14:65188600-65193600	Enhancers	Colon Smooth Muscle	Colon
42	chr14:65188800-65195400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr14:65189200-65191400	Genic enhancers	A549	lung
44	chr14:65189200-65192200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr14:65189400-65191600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr14:65189400-65192000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:65189400-65193400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr14:65189600-65191200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr14:65189600-65191400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr14:65189600-65192200	Weak transcription	HSMMtube	muscle

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