Variant report

Variant	rs2678713
Chromosome Location	chr17:45177776-45177777
allele	A/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	IRF3	chr17:45177560-45177831	GM12878	blood:	n/a	chr17:45177651-45177665 chr17:45177716-45177725
2	JUN	chr17:45177052-45177958	K562	blood:	n/a	chr17:45177683-45177692 chr17:45177721-45177732
3	POLR2A	chr17:45177334-45177982	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr17:45177228-45178023	MCF-7	breast:	n/a	n/a
5	POLR2A	chr17:45177354-45177950	SK-N-MC	brain:	n/a	n/a
6	NFATC1	chr17:45177532-45177889	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:45177449-45177966	GM12891	blood:	n/a	n/a
8	POLR2A	chr17:45177255-45178085	GM12878	blood:	n/a	n/a
9	CHD2	chr17:45177441-45177829	H1-hESC	embryonic stem cell:	n/a	n/a
10	TEAD4	chr17:45177465-45177931	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr17:45177420-45177822	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr17:45176887-45178085	Raji	blood:	n/a	n/a
13	POLR2A	chr17:45177340-45177836	K562	blood:	n/a	n/a
14	ZNF143	chr17:45177578-45177786	H1-hESC	embryonic stem cell:	n/a	n/a
15	POU2F2	chr17:45177423-45177965	GM12878	blood:	n/a	n/a
16	FOS	chr17:45177531-45177836	GM12878	blood:	n/a	chr17:45177683-45177692 chr17:45177721-45177732
17	POLR2A	chr17:45177089-45177980	GM12892	blood:	n/a	n/a
18	SP1	chr17:45177270-45178064	A549	lung:	n/a	chr17:45177988-45178002 chr17:45177750-45177759 chr17:45177653-45177662 chr17:45177651-45177663 chr17:45177664-45177675 chr17:45177674-45177695 chr17:45177653-45177662 chr17:45177652-45177661 chr17:45177651-45177662
19	POLR2A	chr17:45177424-45177970	GM12892	blood:	n/a	n/a
20	POLR2A	chr17:45177510-45177930	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr17:45177305-45177954	HepG2	liver:	n/a	n/a
22	POLR2A	chr17:45177328-45177889	HL-60	blood:	n/a	n/a
23	GTF2F1	chr17:45177589-45177950	Hela-S3	cervix:	n/a	n/a
24	YY1	chr17:45177181-45177902	HepG2	liver:	n/a	chr17:45177652-45177661
25	IRF1	chr17:45177536-45177825	K562	blood:	n/a	chr17:45177651-45177665 chr17:45177716-45177725
26	POLR2A	chr17:45177350-45177978	GM12892	blood:	n/a	n/a
27	POLR2A	chr17:45177345-45177992	GM18505	blood:	n/a	n/a
28	HEY1	chr17:45177396-45177884	K562	blood:	n/a	n/a
29	HCFC1	chr17:45177550-45177829	K562	blood:	n/a	n/a
30	POLR2A	chr17:45177333-45177939	HUVEC	blood vessel:	n/a	n/a
31	MAX	chr17:45177378-45177976	A549	lung:	n/a	chr17:45177650-45177660
32	POLR2A	chr17:45177443-45178022	GM12892	blood:	n/a	n/a
33	NR3C1	chr17:45177246-45177944	A549	lung:	n/a	n/a
34	ELF1	chr17:45177505-45177906	HepG2	liver:	n/a	n/a
35	POLR2A	chr17:45177390-45177947	U87	brain:	n/a	n/a
36	MAX	chr17:45177330-45177798	Hela-S3	cervix:	n/a	chr17:45177650-45177660
37	TBP	chr17:45177502-45177869	K562	blood:	n/a	n/a
38	POLR2A	chr17:45177233-45177962	GM19193	blood:	n/a	n/a
39	POU2F2	chr17:45177487-45178046	GM12891	blood:	n/a	n/a
40	ETS1	chr17:45177372-45177903	A549	lung:	n/a	chr17:45177650-45177661
41	TAF1	chr17:45177462-45177989	SK-N-SH	brain:	n/a	n/a
42	TAF1	chr17:45177467-45177968	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr17:45177268-45178019	H1-neurons	neurons:	n/a	n/a
44	MAX	chr17:45177167-45177976	HepG2	liver:	n/a	chr17:45177650-45177660
45	JUND	chr17:45177344-45177945	A549	lung:	n/a	chr17:45177683-45177692 chr17:45177721-45177732
46	REST	chr17:45177627-45177980	HepG2	liver:	n/a	n/a
47	SP2	chr17:45177345-45177996	HepG2	liver:	n/a	chr17:45177683-45177693 chr17:45177647-45177662 chr17:45177664-45177679
48	CHD2	chr17:45177396-45177943	Hela-S3	cervix:	n/a	n/a
49	SP1	chr17:45177223-45178099	HCT-116	colon:	n/a	chr17:45177988-45178002 chr17:45177750-45177759 chr17:45177653-45177662 chr17:45177651-45177663 chr17:45177664-45177675 chr17:45177674-45177695 chr17:45177653-45177662 chr17:45177652-45177661 chr17:45177651-45177662
50	GATA3	chr17:45177721-45177973	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:44302347..44303352-chr17:45177408..45178065,4	HCT-116	colon:

Variant related genes	Relation type
ENSG00000262879	TF binding region
ENSG00000120071	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11079751	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11649831	0.84[ASN][1000 genomes]
rs11650241	0.82[ASN][1000 genomes]
rs12452715	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16941569	0.90[ASN][1000 genomes]
rs35936425	0.84[ASN][1000 genomes]
rs56023235	0.90[ASN][1000 genomes]
rs56200895	0.84[ASN][1000 genomes]
rs57418075	0.84[ASN][1000 genomes]
rs73308962	0.90[ASN][1000 genomes]
rs8067246	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers 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 miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv521632	chr17:45151549-45196190	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv908563	chr17:45158537-45230311	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv962456	chr17:45163689-45212872	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2678713	RP11-156P1.3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45175600-45178200	Active TSS	GM12878-XiMat	blood
2	chr17:45176000-45178000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr17:45176200-45178000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:45176200-45178000	Active TSS	NHLF	lung
5	chr17:45176200-45178200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr17:45176200-45178200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr17:45176200-45178200	Active TSS	Brain Angular Gyrus	brain
8	chr17:45176200-45178200	Active TSS	Fetal Brain Female	brain
9	chr17:45176400-45178000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr17:45176400-45178000	Active TSS	Colonic Mucosa	Colon
11	chr17:45176400-45178200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:45176400-45178400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:45176400-45178400	Active TSS	Brain Germinal Matrix	brain
14	chr17:45176400-45178400	Active TSS	Rectal Smooth Muscle	rectum
15	chr17:45176600-45178000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr17:45176600-45178000	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr17:45176600-45178000	Active TSS	NH-A	brain
18	chr17:45176600-45178000	Active TSS	NHDF-Ad	bronchial
19	chr17:45176600-45178200	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr17:45176600-45178200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr17:45176600-45178200	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr17:45176600-45178200	Active TSS	Brain Anterior Caudate	brain
23	chr17:45176600-45178200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr17:45176600-45178200	Active TSS	HMEC	breast
25	chr17:45176600-45178400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr17:45176800-45178000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr17:45176800-45178000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr17:45176800-45178000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:45176800-45178000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr17:45176800-45178000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:45176800-45178000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:45176800-45178000	Active TSS	Gastric	stomach
33	chr17:45176800-45178000	Active TSS	Pancreas	Pancrea
34	chr17:45176800-45178000	Active TSS	Psoas Muscle	Psoas
35	chr17:45176800-45178000	Active TSS	Right Ventricle	heart
36	chr17:45176800-45178000	Active TSS	Stomach Mucosa	stomach
37	chr17:45176800-45178000	Active TSS	HSMM	muscle
38	chr17:45176800-45178000	Active TSS	HSMMtube	muscle
39	chr17:45176800-45178200	Active TSS	Brain Substantia Nigra	brain
40	chr17:45176800-45178200	Active TSS	Fetal Kidney	kidney
41	chr17:45176800-45178200	Active TSS	Ovary	ovary
42	chr17:45176800-45178200	Active TSS	Right Atrium	heart
43	chr17:45176800-45178200	Active TSS	A549	lung
44	chr17:45177000-45177800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:45177000-45177800	Active TSS	Spleen	Spleen
46	chr17:45177000-45178000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr17:45177000-45178000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:45177000-45178000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr17:45177000-45178000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr17:45177000-45178000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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