Variant report

Variant	rs17855606
Chromosome Location	chr16:31142271-31142272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:73)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:73 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr16:31141580-31142879	MCF-7	breast:	n/a	n/a
2	YY1	chr16:31142271-31142452	HCT-116	colon:	n/a	n/a
3	POLR2A	chr16:31141968-31142616	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr16:31141920-31142783	HCT-116	colon:	n/a	n/a
5	POLR2A	chr16:31141881-31142498	MCF-7	breast:	n/a	n/a
6	GATA3	chr16:31142162-31142510	T-47D	breast:	n/a	n/a
7	POLR2A	chr16:31141904-31142701	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr16:31142254-31142491	H1-hESC	embryonic stem cell:	n/a	n/a
9	NR2F2	chr16:31141713-31142763	MCF-7	breast:	n/a	n/a
10	USF1	chr16:31141716-31142667	HCT-116	colon:	n/a	n/a
11	RAD21	chr16:31142165-31142753	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr16:31141954-31142883	H1-hESC	embryonic stem cell:	n/a	n/a
13	SP1	chr16:31142081-31142565	H1-hESC	embryonic stem cell:	n/a	n/a
14	GABPA	chr16:31142245-31142604	H1-hESC	embryonic stem cell:	n/a	n/a
15	NFIC	chr16:31142052-31142908	ECC-1	luminal epithelium:	n/a	n/a
16	TEAD4	chr16:31142104-31142847	ECC-1	luminal epithelium:	n/a	n/a
17	EP300	chr16:31142058-31142745	ECC-1	luminal epithelium:	n/a	n/a
18	USF1	chr16:31141903-31142663	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr16:31141847-31142725	ECC-1	luminal epithelium:	n/a	n/a
20	CEBPB	chr16:31142088-31142634	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr16:31142229-31142656	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr16:31141896-31142649	MCF-7	breast:	n/a	n/a
23	MAX	chr16:31142116-31142677	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3AK20	chr16:31142021-31142762	MCF-7	breast:	n/a	n/a
25	EP300	chr16:31142091-31142653	T-47D	breast:	n/a	n/a
26	TCF12	chr16:31141934-31142862	ECC-1	luminal epithelium:	n/a	chr16:31142026-31142036
27	HDAC2	chr16:31142077-31142668	MCF-7	breast:	n/a	n/a
28	ZBTB7A	chr16:31141892-31142868	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr16:31141957-31142649	HCT-116	colon:	n/a	n/a
30	TAF1	chr16:31142257-31142487	H1-hESC	embryonic stem cell:	n/a	n/a
31	HDAC2	chr16:31141899-31142671	MCF-7	breast:	n/a	n/a
32	USF1	chr16:31141894-31142700	ECC-1	luminal epithelium:	n/a	n/a
33	TCF12	chr16:31142026-31142759	MCF-7	breast:	n/a	chr16:31142026-31142036
34	NR3C1	chr16:31142162-31142579	ECC-1	luminal epithelium:	n/a	n/a
35	USF1	chr16:31141941-31142484	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZBTB7A	chr16:31141884-31142954	ECC-1	luminal epithelium:	n/a	n/a
37	ELF1	chr16:31141672-31142580	MCF-7	breast:	n/a	n/a
38	GATA3	chr16:31141938-31142720	MCF-7	breast:	n/a	n/a
39	TCF12	chr16:31142261-31142559	H1-hESC	embryonic stem cell:	n/a	n/a
40	EP300	chr16:31141813-31142793	ECC-1	luminal epithelium:	n/a	chr16:31141941-31141957
41	JUND	chr16:31142221-31142407	H1-hESC	embryonic stem cell:	n/a	n/a
42	USF1	chr16:31141905-31142637	HCT-116	colon:	n/a	n/a
43	POLR2A	chr16:31141805-31142684	ECC-1	luminal epithelium:	n/a	n/a
44	EP300	chr16:31142241-31142593	MCF-7	breast:	n/a	n/a
45	FOXA1	chr16:31142247-31142774	T-47D	breast:	n/a	n/a
46	FOXA1	chr16:31142240-31142751	T-47D	breast:	n/a	n/a
47	CHD2	chr16:31142031-31142569	H1-hESC	embryonic stem cell:	n/a	n/a
48	ESR1	chr16:31142221-31142552	T-47D	breast:	n/a	n/a
49	MAX	chr16:31141904-31142721	MCF-7	breast:	n/a	n/a
50	GATA3	chr16:31142013-31142592	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:31140279..31143875-chr16:31189793..31193230,5	MCF-7	breast:
2	chr16:31141207..31143921-chr16:31201382..31203908,3	MCF-7	breast:
3	chr16:31141772..31145245-chr16:31195885..31201101,4	MCF-7	breast:
4	chr16:31085582..31087599-chr16:31140621..31143082,2	MCF-7	breast:
5	chr16:30996340..30997914-chr16:31141373..31143883,2	K562	blood:
6	chr16:31140382..31143325-chr16:31190204..31192069,2	K562	blood:
7	chr16:31138688..31143325-chr16:31188339..31193663,6	K562	blood:
8	chr16:31139340..31148115-chr16:31189133..31193213,16	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261385	TF binding region
ENSG00000099377	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000268863	Chromatin interaction
ENSG00000167395	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11645814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11649030	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17708472	0.93[MEX][hapmap]
rs17880887	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2359674	0.81[MEX][hapmap];0.89[MKK][hapmap]
rs4404083	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs45619735	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56388508	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56404782	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72785546	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72785547	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72785553	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9927295	0.93[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
4	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
5	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
6	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
7	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
8	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
9	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
10	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
11	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
12	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases
13	nsv542900	chr16:31137352-31197027	Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription 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	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17855606	STX1B	cis	parietal	SCAN
rs17855606	YPEL3	cis	cerebellum	SCAN
rs17855606	ZNF668	cis	cerebellum	SCAN
rs17855606	STX1B	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31130400-31145000	Strong transcription	Fetal Brain Female	brain
2	chr16:31130400-31153000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr16:31130600-31144400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr16:31130600-31144800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr16:31130600-31144800	Strong transcription	Thymus	Thymus
6	chr16:31130600-31145000	Weak transcription	Fetal Heart	heart
7	chr16:31130600-31145200	Strong transcription	Fetal Stomach	stomach
8	chr16:31130800-31143800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr16:31130800-31144200	Strong transcription	Liver	Liver
10	chr16:31130800-31145000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr16:31132400-31145800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:31132400-31146000	Weak transcription	Hela-S3	cervix
13	chr16:31133800-31146200	Weak transcription	Fetal Brain Male	brain
14	chr16:31134000-31144200	Weak transcription	HUVEC	blood vessel
15	chr16:31134000-31145600	Weak transcription	Fetal Kidney	kidney
16	chr16:31134600-31144400	Strong transcription	Brain Germinal Matrix	brain
17	chr16:31135400-31144800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr16:31135800-31143200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr16:31135800-31153000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr16:31136600-31143800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr16:31137200-31144200	Strong transcription	Dnd41	blood
22	chr16:31137200-31144400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr16:31137400-31143800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr16:31137400-31144600	Strong transcription	Spleen	Spleen
25	chr16:31138000-31142600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr16:31138000-31144000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr16:31138200-31143400	Strong transcription	Aorta	Aorta
28	chr16:31138200-31143800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr16:31138200-31143800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr16:31138200-31144200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr16:31138200-31144200	Strong transcription	Left Ventricle	heart
32	chr16:31138200-31144400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr16:31138200-31144600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr16:31138200-31145200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr16:31138400-31143800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr16:31138400-31144000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr16:31138400-31144200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr16:31138400-31144800	Strong transcription	Colon Smooth Muscle	Colon
39	chr16:31138600-31142600	Genic enhancers	Fetal Intestine Small	intestine
40	chr16:31138600-31144400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr16:31138600-31144600	Strong transcription	Rectal Smooth Muscle	rectum
42	chr16:31138800-31142600	Genic enhancers	Fetal Intestine Large	intestine
43	chr16:31139000-31142800	Strong transcription	HepG2	liver
44	chr16:31139000-31145000	Genic enhancers	Placenta	Placenta
45	chr16:31139200-31142600	Enhancers	Pancreas	Pancrea
46	chr16:31139400-31142800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr16:31139400-31142800	Enhancers	Stomach Mucosa	stomach
48	chr16:31139400-31145200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr16:31139400-31153200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr16:31139600-31144800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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