Variant report

Variant	rs749235
Chromosome Location	chr5:167743409-167743410
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	ZNF217	chr5:167743099-167743733	MCF-7	breast:	n/a	n/a
2	ARID3A	chr5:167741703-167743613	HepG2	liver:	n/a	n/a
3	SIN3AK20	chr5:167743027-167743882	MCF-7	breast:	n/a	n/a
4	HNF4A	chr5:167742981-167743456	HepG2	liver:	n/a	chr5:167743392-167743400
5	ESR1	chr5:167743183-167743798	T-47D	breast:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
6	POLR2A	chr5:167741693-167743787	HepG2	liver:	n/a	n/a
7	ESR1	chr5:167743182-167743801	T-47D	breast:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
8	TCF12	chr5:167742874-167743988	MCF-7	breast:	n/a	chr5:167743243-167743253
9	TCF12	chr5:167742926-167745425	A549	lung:	n/a	chr5:167744367-167744375 chr5:167744609-167744619 chr5:167743243-167743253
10	RAD21	chr5:167743357-167743773	H1-hESC	embryonic stem cell:	n/a	chr5:167743567-167743580
11	TEAD4	chr5:167743233-167743705	MCF-7	breast:	n/a	n/a
12	ELF1	chr5:167743082-167743833	MCF-7	breast:	n/a	n/a
13	FOXA1	chr5:167742928-167743418	HepG2	liver:	n/a	n/a
14	ESR1	chr5:167743208-167743765	ECC-1	luminal epithelium:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
15	HDAC2	chr5:167743043-167743470	HepG2	liver:	n/a	chr5:167743420-167743429
16	ESR1	chr5:167743064-167743801	T-47D	breast:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
17	GATA3	chr5:167742995-167743936	MCF-7	breast:	n/a	chr5:167743421-167743430 chr5:167743420-167743430
18	POLR2A	chr5:167741579-167745205	MCF10A-Er-Src	breast:	n/a	n/a
19	GATA3	chr5:167743151-167743586	T-47D	breast:	n/a	chr5:167743421-167743430 chr5:167743420-167743430
20	FOXM1	chr5:167742987-167743851	MCF-7	breast:	n/a	n/a
21	NR2F2	chr5:167742549-167743852	MCF-7	breast:	n/a	n/a
22	RAD21	chr5:167743179-167743693	MCF-7	breast:	n/a	chr5:167743567-167743580
23	MYBL2	chr5:167742932-167743423	HepG2	liver:	n/a	n/a
24	RCOR1	chr5:167742904-167743454	HepG2	liver:	n/a	n/a
25	CEBPB	chr5:167743091-167743409	HepG2	liver:	n/a	chr5:167743196-167743207
26	FOXA2	chr5:167743022-167743502	A549	lung:	n/a	n/a
27	FOXA1	chr5:167742950-167743502	HepG2	liver:	n/a	n/a
28	FOXA1	chr5:167743110-167743526	T-47D	breast:	n/a	n/a
29	HDAC2	chr5:167743140-167743805	MCF-7	breast:	n/a	chr5:167743420-167743429
30	ESR1	chr5:167743322-167743738	ECC-1	luminal epithelium:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
31	TCF7L2	chr5:167743295-167743592	MCF-7	breast:	n/a	n/a
32	GATA3	chr5:167743093-167744012	MCF-7	breast:	n/a	chr5:167743421-167743430 chr5:167743420-167743430
33	ESR1	chr5:167743188-167743873	ECC-1	luminal epithelium:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
34	HDAC2	chr5:167743123-167743810	MCF-7	breast:	n/a	chr5:167743420-167743429
35	MYC	chr5:167743309-167743625	MCF-7	breast:	n/a	n/a
36	TEAD4	chr5:167742838-167743452	HepG2	liver:	n/a	n/a
37	ESR1	chr5:167743117-167743818	T-47D	breast:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
38	ESR1	chr5:167743185-167743788	ECC-1	luminal epithelium:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
39	ESR1	chr5:167743231-167743735	T-47D	breast:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
40	EP300	chr5:167743068-167743804	MCF-7	breast:	n/a	chr5:167743656-167743672
41	TEAD4	chr5:167743148-167743847	MCF-7	breast:	n/a	n/a
42	NR2F2	chr5:167743107-167743845	MCF-7	breast:	n/a	n/a
43	FOXA1	chr5:167742919-167743443	HepG2	liver:	n/a	n/a
44	POLR2A	chr5:167742847-167743418	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr5:167742957-167743928	MCF-7	breast:	n/a	n/a
46	TBP	chr5:167742908-167743412	HepG2	liver:	n/a	n/a
47	ESR1	chr5:167743159-167743708	T-47D	breast:	n/a	chr5:167743572-167743587 chr5:167743572-167743589 chr5:167743528-167743543
48	EP300	chr5:167742941-167743469	HepG2	liver:	n/a	n/a
49	MYBL2	chr5:167742930-167743439	HepG2	liver:	n/a	n/a
50	MAX	chr5:167742960-167743860	MCF-7	breast:	n/a	chr5:167743063-167743073

No.	Distal block	Cell Line	Cell type
1	chr5:167720610..167721433-chr5:167743019..167743616,2	MCF-7	breast:
2	chr5:167715928..167721153-chr5:167739241..167745348,16	MCF-7	breast:
3	chr5:167728707..167730873-chr5:167742044..167743599,2	MCF-7	breast:

Variant related genes	Relation type
WWC1	TF binding region
ENSG00000113645	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12522956	0.90[CHB][hapmap]
rs13183865	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112556	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534607	chr5:167661667-168454396	Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv949154	chr5:167691208-168323234	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv5119	chr5:167724987-167766076	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs749235	FOXI1	cis	parietal	SCAN
rs749235	AGGF1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167734200-167746000	Enhancers	Fetal Intestine Large	intestine
2	chr5:167734400-167746600	Enhancers	Fetal Intestine Small	intestine
3	chr5:167738200-167747600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:167738400-167744400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:167739400-167745000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:167739600-167743600	Enhancers	HSMM	muscle
7	chr5:167739600-167745000	Enhancers	Pancreas	Pancrea
8	chr5:167739800-167745200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:167740200-167744400	Weak transcription	Right Atrium	heart
10	chr5:167740200-167744800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:167740200-167745600	Enhancers	NH-A	brain
12	chr5:167740800-167744600	Enhancers	Esophagus	oesophagus
13	chr5:167740800-167744800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr5:167740800-167744800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:167740800-167745200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:167740800-167745200	Enhancers	Stomach Mucosa	stomach
17	chr5:167740800-167745200	Enhancers	HMEC	breast
18	chr5:167740800-167745600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:167740800-167745600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr5:167740800-167747000	Enhancers	Placenta	Placenta
21	chr5:167741000-167744600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:167741000-167744600	Enhancers	Lung	lung
23	chr5:167741000-167745000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:167741000-167745000	Enhancers	NHDF-Ad	bronchial
25	chr5:167741000-167745200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:167741000-167745200	Enhancers	NHLF	lung
27	chr5:167741600-167743800	Enhancers	Fetal Kidney	kidney
28	chr5:167741600-167743800	Flanking Active TSS	HepG2	liver
29	chr5:167741600-167744600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr5:167741600-167744600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:167741600-167744800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr5:167741600-167744800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr5:167741600-167745000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:167741600-167745000	Enhancers	Placenta Amnion	Placenta Amnion
35	chr5:167741600-167746000	Enhancers	Fetal Lung	lung
36	chr5:167741800-167743800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr5:167741800-167744000	Enhancers	Brain Anterior Caudate	brain
38	chr5:167741800-167744600	Enhancers	Fetal Brain Male	brain
39	chr5:167741800-167745200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr5:167741800-167745200	Enhancers	Fetal Heart	heart
41	chr5:167741800-167751200	Weak transcription	Gastric	stomach
42	chr5:167742000-167743600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr5:167742000-167744800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr5:167742000-167745000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:167742000-167745000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:167742000-167745600	Enhancers	Osteobl	bone
47	chr5:167742200-167744000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:167742200-167744000	Enhancers	GM12878-XiMat	blood
49	chr5:167742200-167744200	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr5:167742400-167743800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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