Variant report

Variant	rs56754638
Chromosome Location	chr4:159098279-159098280
allele	A/G
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	ESR1	chr4:159097903-159098351	T-47D	breast:	n/a	n/a
2	EP300	chr4:159097774-159098439	T-47D	breast:	n/a	n/a
3	SRF	chr4:159097991-159098460	ECC-1	luminal epithelium:	n/a	n/a
4	ESR1	chr4:159097904-159098290	T-47D	breast:	n/a	n/a
5	ESR1	chr4:159097912-159098297	T-47D	breast:	n/a	n/a
6	FOXA1	chr4:159097800-159098283	T-47D	breast:	n/a	n/a
7	NR3C1	chr4:159097946-159098336	ECC-1	luminal epithelium:	n/a	n/a
8	NFIC	chr4:159097868-159098410	ECC-1	luminal epithelium:	n/a	n/a
9	CEBPB	chr4:159097942-159098298	MCF-7	breast:	n/a	n/a
10	GATA3	chr4:159097184-159098454	MCF-7	breast:	n/a	chr4:159098421-159098442
11	ESR1	chr4:159097920-159098281	T-47D	breast:	n/a	n/a
12	SIN3AK20	chr4:159097175-159098491	MCF-7	breast:	n/a	n/a
13	HDAC2	chr4:159097915-159098315	MCF-7	breast:	n/a	n/a
14	JUND	chr4:159097803-159098364	T-47D	breast:	n/a	n/a
15	GATA3	chr4:159097097-159098420	MCF-7	breast:	n/a	n/a
16	ZNF217	chr4:159097918-159098324	MCF-7	breast:	n/a	n/a
17	NR2F2	chr4:159097828-159098309	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
FAM198B	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11936729	1.00[AMR][1000 genomes]
rs11944517	1.00[AMR][1000 genomes]
rs11945640	1.00[AMR][1000 genomes]
rs11946222	1.00[AMR][1000 genomes]
rs55788430	1.00[AMR][1000 genomes]
rs56033321	1.00[AMR][1000 genomes]
rs56167625	1.00[AMR][1000 genomes]
rs57754015	1.00[AMR][1000 genomes]
rs58547264	1.00[AMR][1000 genomes]
rs58624740	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59234905	1.00[AMR][1000 genomes]
rs72967842	1.00[AMR][1000 genomes]
rs72971730	1.00[AMR][1000 genomes]
rs73857535	1.00[AMR][1000 genomes]
rs73857540	1.00[AMR][1000 genomes]
rs73857549	1.00[AMR][1000 genomes]
rs73857576	1.00[AMR][1000 genomes]
rs73857581	1.00[AMR][1000 genomes]
rs73857583	1.00[AMR][1000 genomes]
rs73857587	1.00[AMR][1000 genomes]
rs73857590	1.00[AMR][1000 genomes]
rs73857591	1.00[AMR][1000 genomes]
rs73857593	1.00[AMR][1000 genomes]
rs73857598	1.00[AMR][1000 genomes]
rs7655528	1.00[AMR][1000 genomes]

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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159092600-159104000	Weak transcription	Lung	lung
2	chr4:159093800-159100000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:159094200-159099200	Weak transcription	Placenta	Placenta
4	chr4:159094400-159098400	Enhancers	HMEC	breast
5	chr4:159094400-159103200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:159094600-159098800	Enhancers	Adipose Nuclei	Adipose
7	chr4:159094600-159098800	Enhancers	Fetal Intestine Large	intestine
8	chr4:159094800-159100000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:159095000-159100400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:159095000-159103200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:159095400-159099600	Weak transcription	Brain Substantia Nigra	brain
12	chr4:159095800-159113800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:159096200-159103200	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:159096400-159099200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:159096400-159100800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:159096400-159107400	Weak transcription	HSMMtube	muscle
17	chr4:159096400-159113600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:159096400-159131200	Weak transcription	Right Ventricle	heart
19	chr4:159096400-159131200	Weak transcription	HepG2	liver
20	chr4:159097000-159098400	Enhancers	Fetal Heart	heart
21	chr4:159097000-159098400	Enhancers	Fetal Intestine Small	intestine
22	chr4:159097200-159098800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:159097400-159098400	Enhancers	Brain Cingulate Gyrus	brain
24	chr4:159097400-159098800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr4:159097600-159098400	Enhancers	Brain Angular Gyrus	brain
26	chr4:159097600-159098400	Enhancers	Ovary	ovary
27	chr4:159097800-159099200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:159097800-159099400	Weak transcription	Aorta	Aorta
29	chr4:159097800-159100200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:159097800-159100200	Weak transcription	Right Atrium	heart
31	chr4:159097800-159101000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:159097800-159103200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:159097800-159103200	Weak transcription	Left Ventricle	heart
34	chr4:159097800-159122400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr4:159098000-159098400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:159098000-159098600	Weak transcription	Pancreas	Pancrea
37	chr4:159098000-159098600	Weak transcription	Stomach Mucosa	stomach
38	chr4:159098000-159099800	Strong transcription	HSMM	muscle
39	chr4:159098000-159099800	Weak transcription	HUVEC	blood vessel
40	chr4:159098000-159102200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:159098200-159098400	Enhancers	Duodenum Mucosa	Duodenum

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