Variant report

Variant	rs4925046
Chromosome Location	chr17:19656202-19656203
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	SP1	chr17:19655324-19657005	HCT-116	colon:	n/a	chr17:19656877-19656884
2	MAX	chr17:19656103-19657637	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr17:19655245-19657642	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr17:19656040-19656796	Hela-S3	cervix:	n/a	n/a
5	RPC155	chr17:19655558-19656331	Hela-S3	cervix:	n/a	n/a
6	BCL3	chr17:19655518-19657605	A549	lung:	n/a	n/a
7	POLR2A	chr17:19656148-19656946	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr17:19656138-19656755	A549	lung:	n/a	n/a
9	CTCF	chr17:19655567-19657796	A549	lung:	n/a	chr17:19657361-19657374 chr17:19657354-19657367 chr17:19657352-19657370
10	POLR2A	chr17:19655337-19656871	Hela-S3	cervix:	n/a	n/a
11	MAX	chr17:19655360-19657497	A549	lung:	n/a	n/a
12	JUND	chr17:19655232-19656876	A549	lung:	n/a	chr17:19656544-19656554 chr17:19656545-19656553 chr17:19656389-19656396 chr17:19656544-19656554
13	TCF12	chr17:19655127-19657555	A549	lung:	n/a	chr17:19657317-19657324 chr17:19657316-19657326
14	POLR2A	chr17:19655545-19656753	A549	lung:	n/a	n/a
15	STAT1	chr17:19655498-19657628	Hela-S3	cervix:	n/a	chr17:19656450-19656458 chr17:19657410-19657421
16	POLR2A	chr17:19655742-19656801	ECC-1	luminal epithelium:	n/a	n/a
17	JUND	chr17:19656179-19656936	A549	lung:	n/a	chr17:19656544-19656554 chr17:19656545-19656553 chr17:19656389-19656396 chr17:19656544-19656554 chr17:19656884-19656896
18	NFIC	chr17:19655190-19656954	ECC-1	luminal epithelium:	n/a	n/a
19	TCF12	chr17:19656059-19656950	SK-N-SH	brain:	n/a	n/a
20	ZBTB33	chr17:19656155-19656931	A549	lung:	n/a	n/a
21	TCF7L2	chr17:19655969-19656717	Hela-S3	cervix:	n/a	chr17:19656545-19656554
22	FOSL2	chr17:19655170-19657625	A549	lung:	n/a	chr17:19656544-19656554 chr17:19656545-19656553 chr17:19656389-19656396 chr17:19656544-19656554 chr17:19656884-19656896
23	USF1	chr17:19656082-19656913	A549	lung:	n/a	n/a
24	REST	chr17:19655838-19657489	A549	lung:	n/a	chr17:19657057-19657067 chr17:19656063-19656081 chr17:19656075-19656088 chr17:19656075-19656088
25	SMARCC2	chr17:19655650-19656749	Hela-S3	cervix:	n/a	chr17:19656545-19656554
26	POLR2A	chr17:19655652-19656810	A549	lung:	n/a	n/a
27	TCF12	chr17:19655317-19657547	ECC-1	luminal epithelium:	n/a	chr17:19657317-19657324 chr17:19657316-19657326
28	SMARCC1	chr17:19655557-19657380	Hela-S3	cervix:	n/a	chr17:19656545-19656554
29	TCF12	chr17:19655162-19657509	ECC-1	luminal epithelium:	n/a	chr17:19657317-19657324 chr17:19657316-19657326
30	EP300	chr17:19655204-19657697	A549	lung:	n/a	chr17:19656968-19656975
31	BCL3	chr17:19655354-19657717	A549	lung:	n/a	n/a
32	TBP	chr17:19656129-19657564	Hela-S3	cervix:	n/a	n/a
33	SP1	chr17:19655099-19657664	A549	lung:	n/a	chr17:19656877-19656884
34	POLR2A	chr17:19656132-19656876	HUVEC	blood vessel:	n/a	n/a
35	GABPA	chr17:19656093-19657020	A549	lung:	n/a	n/a
36	PBX3	chr17:19655890-19656877	A549	lung:	n/a	chr17:19656164-19656173
37	ZBTB7A	chr17:19656135-19656868	ECC-1	luminal epithelium:	n/a	n/a
38	TEAD4	chr17:19656184-19656931	ECC-1	luminal epithelium:	n/a	n/a
39	MAX	chr17:19656165-19656806	MCF-7	breast:	n/a	n/a
40	ATF3	chr17:19655686-19657537	A549	lung:	n/a	n/a
41	POLR2A	chr17:19656148-19656733	A549	lung:	n/a	n/a
42	BHLHE40	chr17:19655484-19656735	A549	lung:	n/a	n/a
43	ATF3	chr17:19656201-19656926	A549	lung:	n/a	n/a
44	NFIC	chr17:19656167-19656922	SK-N-SH	brain:	n/a	n/a
45	HDAC2	chr17:19656097-19656797	MCF-7	breast:	n/a	n/a
46	MAFK	chr17:19656007-19657498	Hela-S3	cervix:	n/a	chr17:19656983-19656997 chr17:19656350-19656359 chr17:19656057-19656073 chr17:19656985-19656996 chr17:19656985-19656996 chr17:19656984-19656995 chr17:19656984-19656995
47	NR3C1	chr17:19655495-19656799	A549	lung:	n/a	chr17:19656067-19656082 chr17:19656545-19656554
48	TEAD4	chr17:19656193-19657637	A549	lung:	n/a	n/a
49	FOXA2	chr17:19655817-19656801	A549	lung:	n/a	n/a
50	SIN3AK20	chr17:19655842-19657513	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:67397857..67399603-chr17:19654494..19656370,2	MCF-7	breast:
2	chr17:19621105..19622742-chr17:19656130..19658211,2	MCF-7	breast:
3	chr11:67406449..67409216-chr17:19654457..19656822,7	MCF-7	breast:
4	chr17:19641453..19644108-chr17:19654195..19656369,2	MCF-7	breast:
5	chr11:67397006..67400354-chr17:19655005..19658242,3	MCF-7	breast:
6	chr11:67405096..67409176-chr17:19654881..19658832,8	MCF-7	breast:
7	chr11:67139722..67141643-chr17:19656038..19657945,2	MCF-7	breast:
8	chr11:67407271..67408048-chr17:19655503..19656398,3	MCF-7	breast:
9	chr17:19651262..19653097-chr17:19654120..19656277,2	K562	blood:
10	chr17:19649191..19653636-chr17:19654131..19659903,8	MCF-7	breast:
11	chr11:67382088..67384067-chr17:19655991..19658673,2	MCF-7	breast:
12	chr11:67380849..67383590-chr17:19654631..19658826,3	MCF-7	breast:

Variant related genes	Relation type
ALDH3A1	TF binding region
ENSG00000230607	TF binding region
ENSG00000175505	Chromatin interaction
ENSG00000167799	Chromatin interaction
ENSG00000256514	Chromatin interaction
ENSG00000262681	Chromatin interaction
ENSG00000108602	Chromatin interaction
ENSG00000167800	Chromatin interaction
ENSG00000180638	Chromatin interaction
ENSG00000231793	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs118943	0.88[MEX][hapmap]
rs150122	0.88[MEX][hapmap]
rs157395	0.88[MEX][hapmap]
rs157396	0.88[MEX][hapmap]
rs157402	0.88[MEX][hapmap]
rs188138	0.88[MEX][hapmap]
rs205093	0.88[MEX][hapmap]
rs205096	0.88[MEX][hapmap]
rs205107	0.88[MEX][hapmap]
rs205110	0.88[MEX][hapmap]
rs281332	0.88[MEX][hapmap]
rs281342	0.88[MEX][hapmap]
rs281346	0.88[MEX][hapmap]
rs281351	0.88[MEX][hapmap]
rs56794428	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs917519	0.88[MEX][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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv1793043	chr17:19604821-19670329	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv457704	chr17:19620477-19663747	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv470582	chr17:19620477-19663747	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv574580	chr17:19620477-19663747	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1061489	chr17:19654704-19705026	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv112170	chr17:19655486-19662348	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv13337	chr17:19655966-19662464	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19648800-19657000	Weak transcription	Spleen	Spleen
2	chr17:19649000-19656400	Weak transcription	Right Atrium	heart
3	chr17:19650200-19656800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr17:19650600-19657000	Enhancers	HMEC	breast
5	chr17:19650600-19657600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:19652400-19656400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:19652400-19656600	Weak transcription	Pancreas	Pancrea
8	chr17:19652600-19656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:19653400-19657400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:19654400-19658600	Enhancers	Stomach Mucosa	stomach
11	chr17:19654600-19656400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:19654600-19656400	Weak transcription	Lung	lung
13	chr17:19655200-19657200	Enhancers	Fetal Muscle Trunk	muscle
14	chr17:19655200-19657400	Enhancers	Esophagus	oesophagus
15	chr17:19655200-19657400	Enhancers	HSMM	muscle
16	chr17:19655400-19656400	Flanking Active TSS	A549	lung
17	chr17:19655400-19656800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:19655400-19657400	Enhancers	Brain Substantia Nigra	brain
19	chr17:19655400-19657400	Enhancers	Duodenum Mucosa	Duodenum
20	chr17:19655400-19657400	Enhancers	Fetal Muscle Leg	muscle
21	chr17:19655400-19657400	Flanking Active TSS	Hela-S3	cervix
22	chr17:19655400-19657400	Enhancers	HUVEC	blood vessel
23	chr17:19655400-19657400	Enhancers	NHDF-Ad	bronchial
24	chr17:19655400-19657600	Enhancers	HSMMtube	muscle
25	chr17:19655600-19657400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:19655600-19657400	Enhancers	Adipose Nuclei	Adipose
27	chr17:19655600-19657400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr17:19655600-19657400	Enhancers	NH-A	brain
29	chr17:19655800-19656600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:19655800-19656600	Enhancers	Colonic Mucosa	Colon
31	chr17:19655800-19656800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:19655800-19656800	Enhancers	HepG2	liver
33	chr17:19655800-19657000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr17:19655800-19657200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr17:19655800-19657200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr17:19655800-19657400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr17:19655800-19657400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:19655800-19657400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr17:19655800-19657400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr17:19655800-19657400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr17:19655800-19657400	Enhancers	Brain Angular Gyrus	brain
42	chr17:19655800-19657400	Enhancers	Brain Anterior Caudate	brain
43	chr17:19655800-19657400	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr17:19656000-19656800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:19656000-19657200	Flanking Active TSS	NHEK	skin
46	chr17:19656000-19657400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr17:19656000-19657400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr17:19656000-19657400	Enhancers	Gastric	stomach
49	chr17:19656000-19657400	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr17:19656000-19657400	Enhancers	Sigmoid Colon	Sigmoid Colon

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