Variant report

Variant	rs547708225
Chromosome Location	chr3:160822400-160822401
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	GABPA	chr3:160822071-160823714	MCF-7	breast:	n/a	n/a
2	MAX	chr3:160822234-160823527	HCT-116	colon:	n/a	n/a
3	TBP	chr3:160822375-160823386	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr3:160822190-160823454	H1-hESC	embryonic stem cell:	n/a	chr3:160822474-160822483
5	ELF1	chr3:160822220-160823507	MCF-7	breast:	n/a	chr3:160823439-160823450
6	MAX	chr3:160822276-160823468	MCF-7	breast:	n/a	n/a
7	POLR2A	chr3:160822377-160823203	H1-hESC	embryonic stem cell:	n/a	n/a
8	TEAD4	chr3:160822260-160822728	H1-hESC	embryonic stem cell:	n/a	chr3:160822474-160822483
9	MAX	chr3:160822320-160823501	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:160822192-160823442	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:160822260-160822410	AG04449	skin:	n/a	n/a
12	MAX	chr3:160821640-160823909	MCF-7	breast:	n/a	n/a
13	RAD21	chr3:160822293-160822839	H1-hESC	embryonic stem cell:	n/a	n/a
14	HA-E2F1	chr3:160822200-160823635	MCF-7	breast:	n/a	chr3:160823207-160823221 chr3:160823210-160823224 chr3:160822776-160822788
15	BACH1	chr3:160822337-160823250	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:160822386-160823399	MCF-7	breast:	n/a	n/a
17	NANOG	chr3:160822368-160822711	H1-hESC	embryonic stem cell:	n/a	n/a
18	STAT3	chr3:160822366-160822589	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr3:160822362-160822827	H1-hESC	embryonic stem cell:	n/a	n/a
20	E2F6	chr3:160822061-160823742	H1-hESC	embryonic stem cell:	n/a	chr3:160823207-160823221 chr3:160823210-160823224 chr3:160822776-160822788
21	JUND	chr3:160822284-160822834	H1-hESC	embryonic stem cell:	n/a	n/a
22	HDAC2	chr3:160821953-160823716	MCF-7	breast:	n/a	n/a
23	POLR2A	chr3:160822331-160823260	MCF-7	breast:	n/a	n/a
24	CTCF	chr3:160822400-160822550	HRE	kidney:	n/a	n/a
25	CTCF	chr3:160822400-160822550	GM12864	blood:	n/a	n/a
26	USF2	chr3:160822393-160822458	H1-hESC	embryonic stem cell:	n/a	n/a
27	REST	chr3:160822099-160822792	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr3:160822344-160823455	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr3:160822400-160822550	AG04449	skin:	n/a	n/a
30	ZNF143	chr3:160822294-160823227	H1-hESC	embryonic stem cell:	n/a	chr3:160822502-160822512
31	CEBPB	chr3:160822350-160822703	H1-hESC	embryonic stem cell:	n/a	n/a
32	SIN3A	chr3:160822337-160823305	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:160822320-160822962	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr3:160822387-160822996	MCF10A-Er-Src	breast:	n/a	n/a
35	CTCF	chr3:160822280-160822430	AG10803	skin:	n/a	n/a
36	TAF1	chr3:160822292-160823266	H1-hESC	embryonic stem cell:	n/a	n/a
37	E2F6	chr3:160822343-160823545	H1-hESC	embryonic stem cell:	n/a	chr3:160823207-160823221 chr3:160823210-160823224 chr3:160822776-160822788
38	MYC	chr3:160822219-160822585	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:160822375-160822761	U87	brain:	n/a	n/a
40	RAD21	chr3:160822353-160823360	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr3:160822393-160823333	PANC-1	pancreas:	n/a	n/a
42	CTBP2	chr3:160822389-160823317	H1-hESC	embryonic stem cell:	n/a	n/a
43	CHD2	chr3:160822261-160822792	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr3:160822306-160823567	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr3:160822387-160823348	MCF-7	breast:	n/a	n/a
46	MAX	chr3:160822372-160823507	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr3:160822320-160822470	AoAF	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:
3	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:

Variant related genes	Relation type
B3GALNT1	TF binding region
NMD3	TF binding region
ENSG00000196542	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv877705	chr3:160818188-160836006	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877706	chr3:160820175-160826404	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877707	chr3:160820175-160836006	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3420135	chr3:160821883-160824431	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv877708	chr3:160821969-160826404	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv877709	chr3:160822198-160826404	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:151 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160800400-160822400	Weak transcription	Spleen	Spleen
2	chr3:160802600-160822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:160821600-160823200	Active TSS	Right Ventricle	heart
4	chr3:160821800-160822400	Flanking Active TSS	Brain Anterior Caudate	brain
5	chr3:160821800-160823200	Active TSS	Left Ventricle	heart
6	chr3:160821800-160823600	Active TSS	Brain Cingulate Gyrus	brain
7	chr3:160821800-160823600	Active TSS	Fetal Brain Female	brain
8	chr3:160821800-160823600	Active TSS	Stomach Smooth Muscle	stomach
9	chr3:160821800-160823800	Active TSS	Brain Substantia Nigra	brain
10	chr3:160821800-160824200	Active TSS	Fetal Kidney	kidney
11	chr3:160822000-160822400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr3:160822000-160822400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:160822000-160822400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
14	chr3:160822000-160822400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
15	chr3:160822000-160822400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:160822000-160822400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:160822000-160822400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:160822000-160822400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:160822000-160822400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr3:160822000-160822400	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr3:160822000-160822400	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr3:160822000-160822400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr3:160822000-160822400	Flanking Active TSS	Fetal Intestine Small	intestine
24	chr3:160822000-160822400	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr3:160822000-160822400	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr3:160822000-160822400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr3:160822000-160822400	Flanking Active TSS	HUVEC	blood vessel
28	chr3:160822000-160822400	Flanking Active TSS	NH-A	brain
29	chr3:160822000-160822400	Flanking Active TSS	NHEK	skin
30	chr3:160822000-160822600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:160822000-160823000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:160822000-160823000	Active TSS	Esophagus	oesophagus
33	chr3:160822000-160823000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:160822000-160823200	Active TSS	Fetal Muscle Trunk	muscle
35	chr3:160822000-160823200	Active TSS	Ovary	ovary
36	chr3:160822000-160823400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr3:160822000-160823400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:160822000-160823400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
39	chr3:160822000-160823400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:160822000-160823400	Active TSS	Primary T cells from cord blood	blood
41	chr3:160822000-160823400	Active TSS	Muscle Satellite Cultured Cells	--
42	chr3:160822000-160823400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr3:160822000-160823400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:160822000-160823400	Active TSS	Aorta	Aorta
45	chr3:160822000-160823400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:160822000-160823400	Active TSS	Lung	lung
47	chr3:160822000-160823400	Active TSS	Right Atrium	heart
48	chr3:160822000-160823400	Flanking Active TSS	HMEC	breast
49	chr3:160822000-160823600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr3:160822000-160823600	Active TSS	Breast Myoepithelial Primary Cells	Breast

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