Variant report

Variant	rs17108560
Chromosome Location	chr14:71277255-71277256
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:71277163-71277565	HepG2	liver:	n/a	n/a
2	TAF1	chr14:71276452-71277418	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr14:71277142-71277261	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr14:71277231-71277299	H1-hESC	embryonic stem cell:	n/a	n/a
5	GABPA	chr14:71276302-71277351	MCF-7	breast:	n/a	n/a
6	ZNF263	chr14:71274656-71277729	HEK293-T-REx	kidney:	n/a	n/a
7	SIN3A	chr14:71274633-71277438	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr14:71275207-71277617	H1-neurons	neurons:	n/a	chr14:71275345-71275358 chr14:71276765-71276783 chr14:71275275-71275293 chr14:71276246-71276259
9	POLR2A	chr14:71274780-71277257	H1-neurons	neurons:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:71076190..71078982-chr14:71275139..71277878,2	MCF-7	breast:
2	chr14:71102508..71105172-chr14:71277207..71278775,2	MCF-7	breast:
3	chr14:71106760..71110006-chr14:71274602..71279359,4	MCF-7	breast:
4	chr14:70233111..70234704-chr14:71276587..71278198,2	MCF-7	breast:
5	chr14:71218602..71225147-chr14:71276029..71280278,8	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCNX-2	chr14:71277047-71277382	ENSG00000259153.1
2	lnc-PCNX-2	chr14:71276612-71277382	NONHSAT037591
3	lnc-PCNX-2	chr14:71276648-71277391	NONHSAT037592

No data

Variant related genes	Relation type
MAP3K9	TF binding region
ENSG00000006432	Chromatin interaction
ENSG00000100650	Chromatin interaction
ENSG00000245466	Chromatin interaction
ENSG00000259115	Chromatin interaction
ENSG00000133985	Chromatin interaction
ENSG00000240837	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17108416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17108460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17108467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17108485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17108585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17108599	1.00[EUR][1000 genomes]
rs17108609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17108623	1.00[EUR][1000 genomes]
rs17108653	1.00[EUR][1000 genomes]
rs28407359	1.00[EUR][1000 genomes]
rs28744658	1.00[EUR][1000 genomes]
rs34344982	1.00[EUR][1000 genomes]
rs7156877	1.00[AMR][1000 genomes]
rs8003817	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	esv3376635	chr14:71275024-71277572	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71273000-71280600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:71274200-71278800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:71274200-71279400	Active TSS	HMEC	breast
4	chr14:71274400-71277600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr14:71274400-71277800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr14:71274400-71277800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr14:71274400-71278200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr14:71274600-71277600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr14:71274600-71277600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr14:71274600-71277800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr14:71274600-71277800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr14:71274600-71279400	Active TSS	Esophagus	oesophagus
13	chr14:71274800-71277400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr14:71274800-71277400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:71274800-71277400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
16	chr14:71274800-71277600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:71274800-71277600	Active TSS	Brain Anterior Caudate	brain
18	chr14:71274800-71277800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr14:71274800-71277800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:71274800-71278200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr14:71274800-71278600	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr14:71274800-71279400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr14:71275000-71277600	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr14:71275000-71277600	Active TSS	NHEK	skin
25	chr14:71275000-71277800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr14:71275000-71277800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:71275000-71277800	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr14:71275000-71277800	Active TSS	A549	lung
29	chr14:71275200-71277400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:71275200-71277800	Active TSS	Fetal Kidney	kidney
31	chr14:71275200-71278000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
32	chr14:71275600-71277400	Bivalent/Poised TSS	Fetal Stomach	stomach
33	chr14:71276000-71278600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr14:71276400-71277400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr14:71276400-71277400	Flanking Active TSS	Dnd41	blood
36	chr14:71276600-71277400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr14:71276600-71277600	Active TSS	Stomach Mucosa	stomach
38	chr14:71276800-71277400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr14:71276800-71277400	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr14:71276800-71277400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
41	chr14:71276800-71277400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr14:71276800-71277400	Flanking Active TSS	Hela-S3	cervix
43	chr14:71276800-71277400	Bivalent/Poised TSS	HepG2	liver
44	chr14:71276800-71277600	Weak transcription	Small Intestine	intestine
45	chr14:71276800-71278000	Flanking Active TSS	Fetal Brain Female	brain
46	chr14:71277000-71277400	Enhancers	Primary B cells from peripheral blood	blood
47	chr14:71277000-71277400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr14:71277000-71277400	Active TSS	Brain Cingulate Gyrus	brain
49	chr14:71277000-71277400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr14:71277000-71277600	Flanking Active TSS	Duodenum Mucosa	Duodenum

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