Variant report

Variant	rs3828074
Chromosome Location	chr1:113050985-113050986
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	SMARCC1	chr1:113050597-113051570	Hela-S3	cervix:	n/a	n/a
2	MAZ	chr1:113050395-113051734	IMR90	lung:	n/a	n/a
3	MTA3	chr1:113050900-113051373	GM12878	blood:	n/a	n/a
4	SMARCB1	chr1:113050566-113052129	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr1:113050789-113051481	GM12878	blood:	n/a	n/a
6	SP1	chr1:113050962-113051570	A549	lung:	n/a	chr1:113051538-113051547 chr1:113051006-113051016 chr1:113051538-113051547 chr1:113051537-113051549 chr1:113051539-113051548 chr1:113051440-113051452 chr1:113051537-113051549 chr1:113051538-113051552 chr1:113051006-113051015 chr1:113051440-113051452
7	SIN3A	chr1:113049979-113052294	H1-hESC	embryonic stem cell:	n/a	chr1:113050641-113050650 chr1:113051200-113051213 chr1:113050644-113050657
8	ZNF143	chr1:113050983-113051554	GM12878	blood:	n/a	chr1:113051495-113051505 chr1:113050997-113051012
9	ZNF263	chr1:113050418-113051636	HEK293-T-REx	kidney:	n/a	chr1:113050680-113050689
10	CTCF	chr1:113050960-113051110	WERI-Rb-1	eye:	n/a	n/a
11	CTCF	chr1:113050940-113051090	HCPEpiC	choroid plexus:	n/a	n/a
12	ZBTB7A	chr1:113050451-113051666	ECC-1	luminal epithelium:	n/a	chr1:113050886-113050893
13	ZBTB7A	chr1:113050449-113051796	ECC-1	luminal epithelium:	n/a	chr1:113050886-113050893
14	RCOR1	chr1:113050785-113051502	IMR90	lung:	n/a	n/a
15	SIN3AK20	chr1:113050777-113051542	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr1:113050960-113051110	GM12866	blood:	n/a	n/a
17	CTBP2	chr1:113049984-113052188	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF143	chr1:113049933-113052247	H1-hESC	embryonic stem cell:	n/a	chr1:113051495-113051505 chr1:113050997-113051012 chr1:113050284-113050294 chr1:113050519-113050537 chr1:113050652-113050662

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113050916..113052536-chr1:113056260..113057826,2	K562	blood:
2	chr1:113050070..113052532-chr1:113159337..113161675,2	MCF-7	breast:

Variant related genes	Relation type
WNT2B	TF binding region
ENSG00000007341	Chromatin interaction
ENSG00000134245	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11102484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12136566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3790605	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3790606	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1008375	chr1:113028271-113060221	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1009068	chr1:113048992-113057407	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113050000-113052400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:113050200-113051000	Bivalent Enhancer	Fetal Brain Male	brain
3	chr1:113050200-113051200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:113050200-113051400	Flanking Active TSS	Hela-S3	cervix
5	chr1:113050200-113052000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:113050200-113052000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr1:113050200-113052200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr1:113050200-113052200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:113050200-113052200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:113050200-113052200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
11	chr1:113050200-113052400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:113050200-113052400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:113050200-113052400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:113050200-113052800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:113050400-113051000	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
16	chr1:113050400-113051000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr1:113050400-113051000	Enhancers	Lung	lung
18	chr1:113050400-113051000	Active TSS	Ovary	ovary
19	chr1:113050400-113051200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
20	chr1:113050400-113051200	Bivalent Enhancer	Liver	Liver
21	chr1:113050400-113051200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
22	chr1:113050400-113051200	Bivalent Enhancer	Fetal Lung	lung
23	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
24	chr1:113050400-113051400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
26	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
29	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
30	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
32	chr1:113050400-113051400	Bivalent Enhancer	Fetal Heart	heart
33	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
34	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
35	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
36	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Placenta	Placenta
38	chr1:113050400-113051400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
39	chr1:113050400-113051400	Flanking Active TSS	Osteobl	bone
40	chr1:113050400-113051600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:113050400-113051600	Flanking Bivalent TSS/Enh	NH-A	brain
42	chr1:113050400-113051800	Active TSS	H9 Cell Line	embryonic stem cell
43	chr1:113050400-113051800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:113050400-113051800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
45	chr1:113050400-113052000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
46	chr1:113050400-113052000	Flanking Active TSS	Right Ventricle	heart
47	chr1:113050400-113052000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
48	chr1:113050400-113052200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
49	chr1:113050400-113052200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:113050400-113052200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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