Variant report

Variant	rs17108939
Chromosome Location	chr14:39644992-39644993
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	CHD2	chr14:39643769-39645117	Hela-S3	cervix:	n/a	chr14:39644663-39644673
2	MAZ	chr14:39643825-39645302	GM12878	blood:	n/a	chr14:39644996-39645003
3	POLR2A	chr14:39643869-39645235	H1-neurons	neurons:	n/a	n/a
4	WRNIP1	chr14:39643371-39645398	GM12878	blood:	n/a	n/a
5	POLR2A	chr14:39644909-39645001	Gliobla	brain:	n/a	n/a
6	POLR2A	chr14:39643918-39645308	IMR90	lung:	n/a	n/a
7	REST	chr14:39643618-39645414	HepG2	liver:	n/a	chr14:39644625-39644638
8	HSF1	chr14:39643931-39645159	HepG2	liver:	n/a	n/a
9	TCF7L2	chr14:39643929-39645153	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr14:39643127-39645394	K562	blood:	n/a	n/a
11	YY1	chr14:39643907-39645165	SK-N-SH	brain:	n/a	chr14:39644662-39644671 chr14:39644423-39644432 chr14:39644666-39644680 chr14:39644473-39644493 chr14:39644814-39644828
12	POLR2A	chr14:39643326-39645159	Hela-S3	cervix:	n/a	n/a
13	EP300	chr14:39643872-39645078	ECC-1	luminal epithelium:	n/a	chr14:39644123-39644131
14	ELF1	chr14:39643926-39645160	GM12878	blood:	n/a	chr14:39645101-39645112
15	TAF1	chr14:39644890-39645161	PFSK-1	brain:	n/a	n/a
16	EP300	chr14:39643449-39645212	GM12878	blood:	n/a	chr14:39644123-39644131 chr14:39643623-39643637 chr14:39645102-39645116
17	YY1	chr14:39644278-39645024	H1-hESC	embryonic stem cell:	n/a	chr14:39644662-39644671 chr14:39644423-39644432 chr14:39644666-39644680 chr14:39644473-39644493 chr14:39644814-39644828
18	POLR2A	chr14:39643919-39645402	HepG2	liver:	n/a	n/a
19	YY1	chr14:39644157-39645122	A549	lung:	n/a	chr14:39644662-39644671 chr14:39644423-39644432 chr14:39644666-39644680 chr14:39644473-39644493 chr14:39644814-39644828
20	TAF1	chr14:39644800-39645139	Hela-S3	cervix:	n/a	n/a
21	TBL1XR1	chr14:39644967-39645176	K562	blood:	n/a	n/a
22	YY1	chr14:39643945-39645136	GM12892	blood:	n/a	chr14:39644662-39644671 chr14:39644423-39644432 chr14:39644666-39644680 chr14:39644473-39644493 chr14:39644814-39644828
23	MAX	chr14:39643891-39645192	ECC-1	luminal epithelium:	n/a	chr14:39644996-39645003
24	POLR2A	chr14:39643731-39645159	Hela-S3	cervix:	n/a	n/a
25	JUND	chr14:39643885-39645215	MCF-7	breast:	n/a	chr14:39644849-39644863 chr14:39644715-39644724
26	TAF1	chr14:39643768-39645224	ECC-1	luminal epithelium:	n/a	n/a
27	YY1	chr14:39644120-39645156	H1-hESC	embryonic stem cell:	n/a	chr14:39644662-39644671 chr14:39644423-39644432 chr14:39644666-39644680 chr14:39644473-39644493 chr14:39644814-39644828
28	ZNF263	chr14:39643585-39645061	HEK293-T-REx	kidney:	n/a	n/a
29	POLR2A	chr14:39643663-39645232	Hela-S3	cervix:	n/a	n/a
30	CHD2	chr14:39643311-39645153	K562	blood:	n/a	chr14:39644663-39644673
31	ELF1	chr14:39644765-39645162	K562	blood:	n/a	chr14:39645101-39645112
32	POLR2A	chr14:39643862-39645150	K562	blood:	n/a	n/a
33	HDAC2	chr14:39643902-39645193	MCF-7	breast:	n/a	n/a
34	POLR2A	chr14:39643219-39645163	Raji	blood:	n/a	n/a
35	POLR2A	chr14:39643132-39645483	GM12892	blood:	n/a	n/a
36	ELF1	chr14:39644734-39645092	K562	blood:	n/a	n/a
37	MXI1	chr14:39643937-39645211	Hela-S3	cervix:	n/a	n/a
38	SP1	chr14:39643780-39645102	HCT-116	colon:	n/a	chr14:39644374-39644395 chr14:39644661-39644673 chr14:39644662-39644671 chr14:39644663-39644672 chr14:39644270-39644281 chr14:39644663-39644672 chr14:39644331-39644345 chr14:39644291-39644312
39	MYC	chr14:39644870-39645036	HepG2	liver:	n/a	chr14:39644996-39645003
40	POLR2A	chr14:39643640-39645498	GM12892	blood:	n/a	n/a
41	CHD1	chr14:39643485-39645701	IMR90	lung:	n/a	chr14:39644663-39644673
42	TAF1	chr14:39643463-39645263	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr14:39643741-39645327	HepG2	liver:	n/a	n/a
44	MAZ	chr14:39643838-39645269	K562	blood:	n/a	chr14:39644996-39645003
45	YY1	chr14:39643867-39645387	HepG2	liver:	n/a	chr14:39644662-39644671 chr14:39644423-39644432 chr14:39644666-39644680 chr14:39644473-39644493 chr14:39644814-39644828
46	UBTF	chr14:39644006-39645106	K562	blood:	n/a	n/a
47	MXI1	chr14:39643829-39645457	IMR90	lung:	n/a	n/a
48	USF1	chr14:39644863-39645041	GM12878	blood:	n/a	n/a
49	TBP	chr14:39643456-39645226	H1-hESC	embryonic stem cell:	n/a	n/a
50	GABPA	chr14:39644686-39645071	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:39643730..39648156-chr14:39734640..39738499,10	MCF-7	breast:
2	chr14:39642546..39647225-chr14:39733415..39737853,13	MCF-7	breast:
3	chr14:39643409..39646477-chr14:39682252..39685201,4	MCF-7	breast:
4	chr14:39582047..39584964-chr14:39643383..39645099,4	K562	blood:
5	chr14:39582116..39585012-chr14:39643452..39645860,4	MCF-7	breast:
6	chr14:39582528..39584759-chr14:39643385..39645029,2	K562	blood:
7	chr10:32217178..32218897-chr14:39643343..39645172,2	MCF-7	breast:
8	chr14:39642562..39645375-chr14:39698449..39701112,2	MCF-7	breast:
9	chr14:39644686..39646338-chr14:39899658..39902040,2	K562	blood:
10	chr14:39644463..39645283-chr2:24307157..24307928,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAPPC6B-1	chr14:39644983-39645084	ENSG00000259083

Variant related genes	Relation type
PNN	TF binding region
ENSG00000092208	Chromatin interaction
ENSG00000270503	Chromatin interaction
ENSG00000165355	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000150526	Chromatin interaction
ENSG00000115129	Chromatin interaction
ENSG00000165322	Chromatin interaction
ENSG00000258940	Chromatin interaction
ENSG00000258941	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1474875	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1555260	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17092058	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17108852	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17108884	1.00[AMR][1000 genomes]
rs17108885	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17108891	1.00[AMR][1000 genomes]
rs17108905	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17108946	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41407745	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58634862	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59099504	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59245613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59671146	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59884790	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60224924	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60746390	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61170483	1.00[AMR][1000 genomes]
rs6571899	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7144933	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7145653	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7145677	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7145969	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7150364	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8007188	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8009864	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8010386	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8016435	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39643200-39645000	Active TSS	Rectal Smooth Muscle	rectum
2	chr14:39643200-39645200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr14:39643200-39645200	Active TSS	Brain Anterior Caudate	brain
4	chr14:39643200-39645200	Active TSS	Duodenum Mucosa	Duodenum
5	chr14:39643200-39645600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr14:39643200-39645600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr14:39643400-39645000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr14:39643400-39645200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr14:39643400-39645200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:39643400-39645200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:39643400-39645200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:39643400-39645200	Active TSS	Colon Smooth Muscle	Colon
13	chr14:39643400-39645200	Active TSS	HMEC	breast
14	chr14:39643400-39645200	Active TSS	Osteobl	bone
15	chr14:39643400-39645400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr14:39643400-39645400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr14:39643400-39645600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:39643400-39645600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr14:39643400-39645600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr14:39643400-39645600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr14:39643400-39645600	Active TSS	Fetal Intestine Small	intestine
22	chr14:39643400-39645600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr14:39643400-39645800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr14:39643600-39645000	Active TSS	Adipose Nuclei	Adipose
25	chr14:39643600-39645000	Active TSS	A549	lung
26	chr14:39643600-39645200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:39643600-39645200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr14:39643600-39645200	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr14:39643600-39645200	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr14:39643600-39645200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr14:39643600-39645200	Active TSS	Brain Angular Gyrus	brain
32	chr14:39643600-39645200	Active TSS	Brain Hippocampus Middle	brain
33	chr14:39643600-39645200	Active TSS	Brain Substantia Nigra	brain
34	chr14:39643600-39645200	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr14:39643600-39645200	Active TSS	Fetal Kidney	kidney
36	chr14:39643600-39645200	Active TSS	Fetal Stomach	stomach
37	chr14:39643600-39645200	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr14:39643600-39645200	Active TSS	Thymus	Thymus
39	chr14:39643600-39645200	Active TSS	Spleen	Spleen
40	chr14:39643600-39645200	Active TSS	HSMM	muscle
41	chr14:39643600-39645200	Active TSS	NH-A	brain
42	chr14:39643600-39645400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:39643600-39645400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:39643600-39645400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr14:39643600-39645400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr14:39643600-39645400	Active TSS	Muscle Satellite Cultured Cells	--
47	chr14:39643600-39645400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr14:39643600-39645400	Active TSS	Aorta	Aorta
49	chr14:39643600-39645400	Active TSS	Esophagus	oesophagus
50	chr14:39643600-39645400	Active TSS	Ovary	ovary

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