Variant report

Variant	rs4677803
Chromosome Location	chr3:194814686-194814687
allele	C/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	EP300	chr3:194814533-194815825	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr3:194814575-194815793	ECC-1	luminal epithelium:	n/a	n/a
3	ZBTB7A	chr3:194814532-194815734	ECC-1	luminal epithelium:	n/a	chr3:194815174-194815181
4	ZBTB7A	chr3:194814430-194815846	ECC-1	luminal epithelium:	n/a	chr3:194815174-194815181
5	POLR2A	chr3:194814633-194816938	GM12892	blood:	n/a	n/a
6	TCF12	chr3:194814468-194815853	ECC-1	luminal epithelium:	n/a	chr3:194815032-194815042 chr3:194815036-194815043 chr3:194815491-194815498 chr3:194815034-194815041
7	NFIC	chr3:194814586-194815789	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr3:194814518-194816173	ECC-1	luminal epithelium:	n/a	chr3:194814978-194814987
9	EGR1	chr3:194814601-194815322	ECC-1	luminal epithelium:	n/a	n/a
10	ESR1	chr3:194814455-194815663	ECC-1	luminal epithelium:	n/a	chr3:194815092-194815107 chr3:194815091-194815108
11	RAD21	chr3:194814623-194815810	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr3:194814592-194816746	GM12892	blood:	n/a	n/a
13	MAX	chr3:194814624-194815711	ECC-1	luminal epithelium:	n/a	chr3:194814978-194814987
14	TEAD4	chr3:194814494-194815975	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr3:194814682-194816516	GM12892	blood:	n/a	n/a
16	ESR1	chr3:194814449-194815644	ECC-1	luminal epithelium:	n/a	chr3:194815092-194815107 chr3:194815091-194815108
17	NFIC	chr3:194814552-194815852	ECC-1	luminal epithelium:	n/a	n/a
18	ESR1	chr3:194814436-194815689	ECC-1	luminal epithelium:	n/a	chr3:194815092-194815107 chr3:194815091-194815108
19	TCF12	chr3:194814413-194815912	ECC-1	luminal epithelium:	n/a	chr3:194815032-194815042 chr3:194815036-194815043 chr3:194815491-194815498 chr3:194815034-194815041
20	TEAD4	chr3:194814609-194815751	ECC-1	luminal epithelium:	n/a	n/a
21	RUNX3	chr3:194814566-194816213	GM12878	blood:	n/a	n/a
22	ELF1	chr3:194814472-194816591	GM12878	blood:	n/a	chr3:194815997-194816008
23	POLR2A	chr3:194814612-194816268	GM19193	blood:	n/a	n/a
24	ZNF263	chr3:194814532-194815140	HEK293-T-REx	kidney:	n/a	chr3:194815073-194815082 chr3:194814763-194814784

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACAP2-4	chr3:194814472-194814938	NONHSAT094139

Variant related genes	Relation type
XXYLT1-AS1	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10804419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10933695	0.82[ASN][1000 genomes]
rs1353222	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4677661	1.00[CHB][hapmap]
rs6764788	0.82[ASN][1000 genomes]
rs6767698	0.82[ASN][1000 genomes]
rs7627506	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9288754	1.00[CHB][hapmap]
rs9825174	1.00[CHB][hapmap]
rs9827336	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:194801200-194814800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:194801200-194814800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:194802000-194826800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:194803200-194815800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:194804000-194818200	Weak transcription	Right Ventricle	heart
7	chr3:194806800-194826400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:194808400-194817000	Weak transcription	HepG2	liver
9	chr3:194808400-194823000	Weak transcription	Adipose Nuclei	Adipose
10	chr3:194808600-194823000	Weak transcription	K562	blood
11	chr3:194808600-194827000	Weak transcription	Fetal Brain Female	brain
12	chr3:194808800-194815200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:194808800-194816400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:194808800-194816800	Weak transcription	NHEK	skin
15	chr3:194808800-194821400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:194808800-194824800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:194813400-194818000	Weak transcription	HUVEC	blood vessel
18	chr3:194814400-194815200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:194814400-194816000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:194814400-194816400	Enhancers	Thymus	Thymus
21	chr3:194814400-194816600	Flanking Active TSS	GM12878-XiMat	blood
22	chr3:194814400-194817000	Enhancers	Primary B cells from cord blood	blood
23	chr3:194814400-194817200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:194814400-194817400	Enhancers	Fetal Intestine Large	intestine
25	chr3:194814400-194817400	Enhancers	Fetal Intestine Small	intestine
26	chr3:194814400-194817400	Enhancers	Fetal Muscle Leg	muscle
27	chr3:194814400-194823000	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:194814600-194814800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr3:194814600-194814800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr3:194814600-194815000	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr3:194814600-194815000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:194814600-194815000	Flanking Active TSS	Fetal Muscle Trunk	muscle
33	chr3:194814600-194815000	Active TSS	Placenta	Placenta
34	chr3:194814600-194815000	Flanking Active TSS	Fetal Thymus	thymus
35	chr3:194814600-194815000	Enhancers	Spleen	Spleen
36	chr3:194814600-194815000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr3:194814600-194815200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:194814600-194815200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:194814600-194815200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:194814600-194815200	Enhancers	Esophagus	oesophagus
41	chr3:194814600-194815200	Enhancers	Fetal Stomach	stomach
42	chr3:194814600-194815200	Enhancers	Dnd41	blood
43	chr3:194814600-194815200	Flanking Active TSS	Hela-S3	cervix
44	chr3:194814600-194815400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:194814600-194815400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:194814600-194815600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:194814600-194815800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:194814600-194816000	Enhancers	HSMM	muscle
49	chr3:194814600-194816200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:194814600-194816200	Enhancers	Skeletal Muscle Female	skeletal muscle

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