Variant report

Variant	rs17030440
Chromosome Location	chr3:42538514-42538515
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	POLR2A	chr3:42538413-42538939	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:42538422-42538722	Hela-S3	cervix:	n/a	n/a
3	TCF12	chr3:42538459-42539002	ECC-1	luminal epithelium:	n/a	n/a
4	NR3C1	chr3:42538508-42538807	ECC-1	luminal epithelium:	n/a	chr3:42538605-42538618
5	NR3C1	chr3:42538465-42538790	ECC-1	luminal epithelium:	n/a	chr3:42538605-42538618
6	TBP	chr3:42538492-42538812	Hela-S3	cervix:	n/a	n/a
7	EP300	chr3:42538449-42538844	Hela-S3	cervix:	n/a	n/a
8	MAZ	chr3:42538386-42538989	IMR90	lung:	n/a	n/a
9	SP1	chr3:42538437-42538847	A549	lung:	n/a	n/a
10	TEAD4	chr3:42538487-42538974	H1-hESC	embryonic stem cell:	n/a	n/a
11	NR3C1	chr3:42538479-42538944	A549	lung:	n/a	chr3:42538605-42538618
12	GTF2F1	chr3:42538451-42538761	Hela-S3	cervix:	n/a	n/a
13	MAZ	chr3:42538497-42538866	Hela-S3	cervix:	n/a	n/a
14	EP300	chr3:42538345-42539115	ECC-1	luminal epithelium:	n/a	chr3:42538406-42538420
15	ZNF263	chr3:42538433-42539189	HEK293-T-REx	kidney:	n/a	chr3:42538816-42538825
16	EP300	chr3:42538404-42538829	A549	lung:	n/a	chr3:42538406-42538420
17	GATA3	chr3:42538341-42538743	T-47D	breast:	n/a	n/a
18	SP1	chr3:42538356-42538868	H1-hESC	embryonic stem cell:	n/a	n/a
19	TAF1	chr3:42538498-42538846	Hela-S3	cervix:	n/a	n/a
20	ZNF143	chr3:42538466-42538788	H1-hESC	embryonic stem cell:	n/a	n/a
21	CHD2	chr3:42538470-42538974	H1-hESC	embryonic stem cell:	n/a	n/a
22	BRCA1	chr3:42538376-42538772	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:42538454-42539033	ECC-1	luminal epithelium:	n/a	n/a
24	MAX	chr3:42538470-42538740	Hela-S3	cervix:	n/a	n/a
25	EP300	chr3:42538421-42539168	ECC-1	luminal epithelium:	n/a	n/a
26	RCOR1	chr3:42538495-42538834	Hela-S3	cervix:	n/a	n/a
27	TEAD4	chr3:42538456-42539125	ECC-1	luminal epithelium:	n/a	n/a
28	TEAD4	chr3:42538427-42538955	H1-hESC	embryonic stem cell:	n/a	n/a
29	KAP1	chr3:42538315-42538977	HEK293	kidney:	n/a	n/a
30	TCF12	chr3:42538362-42539076	ECC-1	luminal epithelium:	n/a	n/a
31	SMC3	chr3:42538474-42538831	Hela-S3	cervix:	n/a	chr3:42538498-42538505
32	TEAD4	chr3:42538330-42539142	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42518620..42520531-chr3:42538511..42540228,2	MCF-7	breast:
2	chr3:42531149..42533028-chr3:42536524..42539427,2	K562	blood:
3	chr3:42538031..42540547-chr3:42542886..42545653,3	MCF-7	breast:

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4467424	1.00[MEX][hapmap]
rs56775805	1.00[EUR][1000 genomes]
rs7613206	1.00[MEX][hapmap]
rs7628932	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42532200-42538800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:42532600-42538600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:42532600-42538800	Weak transcription	Esophagus	oesophagus
4	chr3:42533800-42538600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:42534000-42538600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:42534000-42539600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:42534200-42538600	Weak transcription	Gastric	stomach
8	chr3:42534200-42538600	Weak transcription	Stomach Mucosa	stomach
9	chr3:42534800-42538600	Weak transcription	Right Atrium	heart
10	chr3:42534800-42542800	Weak transcription	Right Ventricle	heart
11	chr3:42535000-42538800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:42535000-42543000	Weak transcription	Left Ventricle	heart
13	chr3:42535200-42538600	Weak transcription	Placenta	Placenta
14	chr3:42535200-42542800	Weak transcription	Pancreas	Pancrea
15	chr3:42535600-42538600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:42535600-42538600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:42535600-42538600	Weak transcription	GM12878-XiMat	blood
18	chr3:42535600-42538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:42535600-42538800	Weak transcription	Spleen	Spleen
20	chr3:42535600-42543000	Weak transcription	Lung	lung
21	chr3:42537000-42539000	Enhancers	Fetal Intestine Large	intestine
22	chr3:42537200-42538600	Enhancers	Duodenum Mucosa	Duodenum
23	chr3:42537600-42539800	Enhancers	Fetal Intestine Small	intestine
24	chr3:42537800-42538600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:42537800-42538800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr3:42537800-42539200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:42537800-42539600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:42538000-42538800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:42538000-42538800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:42538000-42538800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:42538000-42538800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr3:42538000-42539200	Enhancers	HepG2	liver
33	chr3:42538000-42539200	Enhancers	HSMMtube	muscle
34	chr3:42538000-42539200	Enhancers	NH-A	brain
35	chr3:42538000-42540400	Enhancers	Fetal Heart	heart
36	chr3:42538200-42539000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:42538400-42538600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:42538400-42538600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
39	chr3:42538400-42538600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr3:42538400-42538600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr3:42538400-42538600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:42538400-42538600	Enhancers	Adipose Nuclei	Adipose
43	chr3:42538400-42538800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr3:42538400-42538800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
45	chr3:42538400-42538800	Active TSS	Brain Anterior Caudate	brain
46	chr3:42538400-42538800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr3:42538400-42538800	Active TSS	A549	lung
48	chr3:42538400-42538800	Enhancers	HSMM	muscle
49	chr3:42538400-42539000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:42538400-42539000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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