Variant report

Variant	rs1837366
Chromosome Location	chr2:111874629-111874630
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	CTCF	chr2:111874546-111874909	ProgFib	skin:	n/a	chr2:111874765-111874786
2	RAD21	chr2:111874497-111874982	HepG2	liver:	n/a	chr2:111874765-111874779 chr2:111874764-111874783 chr2:111874715-111874722
3	CTCF	chr2:111874582-111874865	K562	blood:	n/a	chr2:111874765-111874786
4	RCOR1	chr2:111874582-111875975	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr2:111874605-111874983	IMR90	lung:	n/a	n/a
6	CTCF	chr2:111873049-111875558	A549	lung:	n/a	chr2:111875132-111875153 chr2:111874765-111874786 chr2:111875130-111875148 chr2:111873712-111873728 chr2:111875135-111875143
7	CTCF	chr2:111874608-111874917	Gliobla	brain:	n/a	chr2:111874765-111874786
8	CTCF	chr2:111874595-111874908	MCF-7	breast:	n/a	chr2:111874765-111874786
9	TEAD4	chr2:111874448-111875023	H1-hESC	embryonic stem cell:	n/a	n/a
10	NFIC	chr2:111874308-111876064	ECC-1	luminal epithelium:	n/a	n/a
11	YY1	chr2:111874624-111874920	HCT-116	colon:	n/a	n/a
12	CTCF	chr2:111874592-111874917	A549	lung:	n/a	chr2:111874765-111874786
13	YY1	chr2:111874525-111874921	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr2:111874459-111875060	MCF-7	breast:	n/a	chr2:111874765-111874786
15	CTCF	chr2:111874628-111874904	LNCaP	prostate:	n/a	chr2:111874765-111874786
16	CTCF	chr2:111874618-111874909	GM13977	blood:	n/a	chr2:111874765-111874786
17	SMARCB1	chr2:111874466-111876366	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr2:111874564-111874936	SK-N-SH_RA	brain:	n/a	chr2:111874765-111874779 chr2:111874764-111874783 chr2:111874715-111874722
19	MAZ	chr2:111874588-111875014	GM12878	blood:	n/a	n/a
20	MAX	chr2:111874351-111875744	MCF-7	breast:	n/a	n/a
21	NFIC	chr2:111874578-111874974	HepG2	liver:	n/a	n/a
22	SMC3	chr2:111874401-111875372	SK-N-SH	brain:	n/a	chr2:111874765-111874779
23	TBP	chr2:111874559-111875234	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr2:111874490-111874992	H1-hESC	embryonic stem cell:	n/a	chr2:111874765-111874786
25	RAD21	chr2:111874555-111874959	GM12878	blood:	n/a	chr2:111874765-111874779 chr2:111874764-111874783 chr2:111874715-111874722
26	MAX	chr2:111874534-111876269	A549	lung:	n/a	n/a
27	MAZ	chr2:111874559-111875020	HepG2	liver:	n/a	n/a
28	RCOR1	chr2:111874425-111874987	HepG2	liver:	n/a	n/a
29	CTCF	chr2:111874600-111874750	A549	lung:	n/a	n/a
30	ZEB1	chr2:111874428-111874923	GM12878	blood:	n/a	chr2:111874722-111874733
31	CTCF	chr2:111874599-111874910	MCF-7	breast:	n/a	chr2:111874765-111874786
32	CHD2	chr2:111874610-111874948	GM12878	blood:	n/a	n/a
33	GABPA	chr2:111874535-111875009	MCF-7	breast:	n/a	n/a
34	CTCF	chr2:111874453-111875114	HCT-116	colon:	n/a	chr2:111874765-111874786
35	FOXM1	chr2:111874464-111875032	MCF-7	breast:	n/a	n/a
36	MYC	chr2:111874598-111874664	MCF-7	breast:	n/a	n/a
37	ZNF263	chr2:111874495-111875425	HEK293-T-REx	kidney:	n/a	chr2:111874852-111874873 chr2:111874814-111874835
38	FOXP2	chr2:111874557-111874791	SK-N-MC	brain:	n/a	n/a
39	ZNF143	chr2:111874417-111875277	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr2:111874538-111874910	ECC-1	luminal epithelium:	n/a	chr2:111874765-111874786
41	CTCF	chr2:111874616-111874922	NHEK	skin:	n/a	chr2:111874765-111874786
42	SMARCC1	chr2:111874583-111876622	Hela-S3	cervix:	n/a	n/a
43	SIN3A	chr2:111874494-111875365	H1-hESC	embryonic stem cell:	n/a	chr2:111874528-111874542
44	CTCF	chr2:111874596-111874915	MCF-7	breast:	n/a	chr2:111874765-111874786
45	TBL1XR1	chr2:111873466-111875169	GM12878	blood:	n/a	n/a
46	CTBP2	chr2:111874524-111881050	H1-hESC	embryonic stem cell:	n/a	n/a
47	SPI1	chr2:111874584-111875048	HL-60	blood:	n/a	n/a
48	MXI1	chr2:111874527-111875159	H1-hESC	embryonic stem cell:	n/a	n/a
49	MXI1	chr2:111873483-111874911	GM12878	blood:	n/a	n/a
50	GATA3	chr2:111874317-111875545	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:111807803..111810295-chr2:111873286..111875323,2	MCF-7	breast:
2	chr2:111786376..111787035-chr2:111873340..111875017,8	MCF-7	breast:
3	chr2:111611685..111612458-chr2:111874292..111875234,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204581	TF binding region
BCL2L11	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10166773	0.87[JPT][hapmap]
rs10189015	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10211562	0.82[ASN][1000 genomes]
rs1054873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13398360	0.86[JPT][hapmap]
rs1439287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837368	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877331	0.80[CHB][hapmap]
rs2241841	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241844	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3789061	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789064	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3789065	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789068	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4302219	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4627572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849403	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56952027	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60286362	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6708784	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6726007	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs6732491	0.86[JPT][hapmap]
rs6734942	0.87[ASN][1000 genomes]
rs6760053	0.91[JPT][hapmap]
rs7577824	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593638	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7602904	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv874842	chr2:111870220-111892984	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111860200-111875000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:111874000-111874800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr2:111874000-111874800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:111874000-111874800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
5	chr2:111874000-111874800	Bivalent Enhancer	Fetal Intestine Small	intestine
6	chr2:111874400-111874800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
7	chr2:111874400-111874800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr2:111874400-111874800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:111874400-111874800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:111874400-111874800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:111874400-111874800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
12	chr2:111874400-111874800	Bivalent Enhancer	Primary B cells from cord blood	blood
13	chr2:111874400-111874800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
14	chr2:111874400-111874800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
15	chr2:111874400-111874800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:111874400-111874800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
17	chr2:111874400-111874800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:111874400-111874800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
19	chr2:111874400-111874800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:111874400-111874800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
21	chr2:111874400-111874800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:111874400-111874800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:111874400-111874800	Enhancers	Adipose Nuclei	Adipose
24	chr2:111874400-111874800	Enhancers	Liver	Liver
25	chr2:111874400-111874800	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr2:111874400-111874800	Enhancers	Esophagus	oesophagus
27	chr2:111874400-111874800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr2:111874400-111874800	Bivalent Enhancer	Fetal Intestine Large	intestine
29	chr2:111874400-111874800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr2:111874400-111874800	Bivalent Enhancer	Fetal Muscle Leg	muscle
31	chr2:111874400-111874800	Enhancers	Placenta	Placenta
32	chr2:111874400-111874800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
33	chr2:111874400-111874800	Bivalent Enhancer	NH-A	brain
34	chr2:111874400-111874800	Bivalent Enhancer	NHDF-Ad	bronchial
35	chr2:111874400-111875000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:111874400-111875000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
37	chr2:111874400-111875000	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
38	chr2:111874400-111875000	Bivalent Enhancer	Fetal Lung	lung
39	chr2:111874400-111875000	Bivalent Enhancer	Fetal Thymus	thymus
40	chr2:111874400-111875000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
41	chr2:111874400-111875200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr2:111874400-111875200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:111874400-111875200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr2:111874400-111875200	Flanking Bivalent TSS/Enh	HepG2	liver
45	chr2:111874400-111875600	Active TSS	A549	lung
46	chr2:111874400-111875800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:111874400-111875800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr2:111874400-111876000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr2:111874400-111876000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
50	chr2:111874400-111876200	Active TSS	Brain Anterior Caudate	brain

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