Variant report

Variant	rs62336790
Chromosome Location	chr4:53728000-53728001
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	RCOR1	chr4:53727953-53728884	K562	blood:	n/a	n/a
2	GATA3	chr4:53727874-53728251	T-47D	breast:	n/a	n/a
3	EGR1	chr4:53727993-53728525	K562	blood:	n/a	chr4:53728435-53728445 chr4:53728430-53728443 chr4:53728430-53728443 chr4:53728429-53728444
4	FOXP2	chr4:53727997-53728715	PFSK-1	brain:	n/a	n/a
5	TBP	chr4:53727916-53728704	K562	blood:	n/a	n/a
6	CHD2	chr4:53727863-53728052	H1-hESC	embryonic stem cell:	n/a	n/a
7	HA-E2F1	chr4:53727679-53728844	MCF-7	breast:	n/a	chr4:53728200-53728210 chr4:53728435-53728444 chr4:53728439-53728449
8	RAD21	chr4:53727978-53728887	SK-N-SH_RA	brain:	n/a	n/a
9	ZBTB7A	chr4:53727992-53728512	ECC-1	luminal epithelium:	n/a	n/a
10	FOXA1	chr4:53727930-53728239	T-47D	breast:	n/a	n/a
11	E2F6	chr4:53727459-53729023	H1-hESC	embryonic stem cell:	n/a	chr4:53728200-53728210 chr4:53728643-53728654 chr4:53728435-53728444 chr4:53728439-53728449
12	ZC3H11A	chr4:53727957-53728000	K562	blood:	n/a	n/a
13	MAZ	chr4:53727966-53728744	K562	blood:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
14	CTCF	chr4:53728000-53728150	HFF	foreskin:	n/a	n/a
15	POLR2A	chr4:53727996-53728747	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr4:53727921-53728922	HEK293	kidney:	n/a	n/a
17	PAX5	chr4:53727914-53728444	GM12878	blood:	n/a	n/a
18	MAX	chr4:53727606-53729106	ECC-1	luminal epithelium:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
19	RAD21	chr4:53727676-53728947	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr4:53727917-53728831	GM12878	blood:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
21	BACH1	chr4:53727935-53728565	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr4:53727599-53729010	H1-hESC	embryonic stem cell:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
23	MAX	chr4:53727927-53728998	SK-N-SH	brain:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
24	SETDB1	chr4:53727772-53729028	K562	blood:	n/a	n/a
25	POLR2A	chr4:53727983-53728811	K562	blood:	n/a	n/a
26	MAX	chr4:53727977-53728886	SK-N-SH	brain:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
27	E2F6	chr4:53727950-53729015	K562	blood:	n/a	chr4:53728200-53728210 chr4:53728643-53728654 chr4:53728435-53728444 chr4:53728439-53728449
28	SIN3A	chr4:53726721-53729851	H1-hESC	embryonic stem cell:	n/a	n/a
29	MYC	chr4:53727977-53728991	K562	blood:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
30	EGR1	chr4:53727983-53728533	K562	blood:	n/a	chr4:53728435-53728445 chr4:53728430-53728443 chr4:53728430-53728443 chr4:53728429-53728444
31	PAX5	chr4:53727964-53728634	GM12892	blood:	n/a	n/a
32	CCNT2	chr4:53727778-53728985	K562	blood:	n/a	chr4:53728435-53728444
33	NFIC	chr4:53727998-53728497	ECC-1	luminal epithelium:	n/a	n/a
34	MXI1	chr4:53726951-53732052	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr4:53727839-53728873	MCF-7	breast:	n/a	n/a
36	MAX	chr4:53727604-53729043	ECC-1	luminal epithelium:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
37	MXI1	chr4:53727567-53729029	IMR90	lung:	n/a	n/a
38	POLR2A	chr4:53727789-53729591	H1-hESC	embryonic stem cell:	n/a	n/a
39	E2F6	chr4:53727777-53729216	K562	blood:	n/a	chr4:53728200-53728210 chr4:53728643-53728654 chr4:53728435-53728444 chr4:53728439-53728449
40	UBTF	chr4:53727980-53728370	K562	blood:	n/a	n/a
41	CTBP2	chr4:53727338-53729596	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr4:53727627-53729027	K562	blood:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
43	MAZ	chr4:53727655-53728836	IMR90	lung:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
44	MAX	chr4:53727662-53728900	H1-hESC	embryonic stem cell:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
45	REST	chr4:53727581-53729044	H1-neurons	neurons:	n/a	chr4:53728200-53728213 chr4:53728894-53728907 chr4:53728081-53728091 chr4:53728200-53728213
46	POLR2A	chr4:53727910-53728939	SK-N-MC	brain:	n/a	n/a
47	POLR2A	chr4:53727744-53729128	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr4:53727834-53728989	MCF-7	breast:	n/a	n/a
49	RAD21	chr4:53727407-53729218	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr4:53727875-53728934	MCF-7	breast:	n/a	chr4:53728303-53728313 chr4:53728433-53728443

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:53727979-53728029	HepG2	liver:	n/a
2	chr4:53727979-53728029	T-47D	breast:	n/a
3	chr4:53727979-53728029	HEK293	kidney:	embryo
4	chr4:53727979-53728029	HAEpiC	amniotic membrane:	n/a
5	chr4:53727979-53728029	HPAEpiC	pulmonary alveolar:	n/a
6	chr4:53727979-53728029	AG09319	gingival:	n/a
7	chr4:53727979-53728029	AG09309	skin:	n/a
8	chr4:53727979-53728029	HNPCEpiC	eye:	n/a
9	chr4:53727979-53728029	GM06990	blood:	n/a
10	chr4:53727979-53728029	K562	blood:	n/a
11	chr4:53727979-53728029	HRE	kidney:	n/a
12	chr4:53727979-53728029	NH-A	brain:	n/a
13	chr4:53727979-53728029	BJ	skin:	n/a
14	chr4:53727979-53728029	ovcar-3	ovarian:	n/a
15	chr4:53727979-53728029	HL-60	blood:	n/a
16	chr4:53727979-53728029	AG04450	lung:	fetal
17	chr4:53727979-53728029	ECC-1	luminal epithelium:	n/a
18	chr4:53727979-53728029	MCF10A-Er-Src	breast:	n/a
19	chr4:53727979-53728029	Hepatocyte	liver:	n/a
20	chr4:53727979-53728029	GM12878	blood:	n/a
21	chr4:53727979-53728029	ProgFib	skin:	n/a
22	chr4:53727979-53728029	HUVEC	blood vessel:	n/a
23	chr4:53727979-53728029	SK-N-SH_RA	brain:	n/a
24	chr4:53727979-53728029	GM12891	blood:	n/a
25	chr4:53727979-53728029	CMK	blood:	n/a
26	chr4:53727979-53728029	NHBE	bronchial:	n/a
27	chr4:53727979-53728029	NB4	blood:	n/a
28	chr4:53727979-53728029	A549	lung:	n/a
29	chr4:53727979-53728029	NT2-D1	testis:	n/a
30	chr4:53727979-53728029	MCF-7	breast:	n/a
31	chr4:53727979-53728029	GM12892	blood:	n/a
32	chr4:53727979-53728029	NHDF-neo	bronchial:	n/a
33	chr4:53727979-53728029	LNCaP	prostate:	n/a
34	chr4:53727979-53728029	HRCEpiC	kidney:	n/a
35	chr4:53727979-53728029	SKMC	muscle:	n/a
36	chr4:53727979-53728029	H1-hESC	embryonic stem cell:	embryo
37	chr4:53727979-53728029	SK-N-MC	brain:	n/a
38	chr4:53727979-53728029	HRPEpiC	eye:	n/a
39	chr4:53727979-53728029	AoSMC	blood vessel:	n/a
40	chr4:53727979-53728029	HCPEpiC	choroid plexus:	n/a
41	chr4:53727979-53728029	AG04449	skin:	fetal
42	chr4:53727979-53728029	HEEpiC	esophagus:	n/a
43	chr4:53727979-53728029	HCM	heart:	n/a
44	chr4:53727979-53728029	Hela-S3	cervix:	n/a
45	chr4:53727979-53728029	RPTEC	kidney:	n/a
46	chr4:53727979-53728029	Caco-2	colon:	n/a
47	chr4:53727979-53728029	GM19239	blood:	n/a
48	chr4:53727979-53728029	U87	brain:	n/a
49	chr4:53727979-53728029	BE2_C	brain:	n/a
50	chr4:53727979-53728029	IMR90	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr4:53525430..53527688-chr4:53726700..53729187,4	MCF-7	breast:
2	chr4:53586938..53589965-chr4:53727574..53731676,3	MCF-7	breast:
3	chr4:53577401..53580169-chr4:53726393..53730142,5	MCF-7	breast:

Variant related genes	Relation type
RASL11B	TF binding region
RASL11B	CpG island
ENSG00000226950	Chromatin interaction
ENSG00000264585	Chromatin interaction
ENSG00000109189	Chromatin interaction
ENSG00000248375	Chromatin interaction
ENSG00000248866	Chromatin interaction
ENSG00000212588	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10003908	0.83[AMR][1000 genomes]
rs10016904	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10023440	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10026162	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10032190	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11940896	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11941841	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11947787	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2017237	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4864676	0.82[AMR][1000 genomes]
rs4864678	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4864680	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864685	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864688	0.80[EUR][1000 genomes]
rs59649036	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62336795	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62338810	0.86[ASN][1000 genomes]
rs6554056	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6839084	0.80[EUR][1000 genomes]
rs6844680	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6852148	0.80[EUR][1000 genomes]
rs730246	0.85[AMR][1000 genomes]
rs730247	0.85[AMR][1000 genomes]
rs731073	0.85[AMR][1000 genomes]
rs7663943	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7692692	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8287	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs881743	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936690	0.86[AMR][1000 genomes]
rs962416	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9995861	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3360858	chr4:53727420-53729968	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:178 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53720600-53728000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:53726800-53728000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr4:53726800-53728000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr4:53727200-53728000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:53727200-53728000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
6	chr4:53727200-53728200	Flanking Active TSS	Fetal Heart	heart
7	chr4:53727400-53728000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:53727400-53728000	Enhancers	Spleen	Spleen
9	chr4:53727400-53728200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:53727400-53729600	Active TSS	Brain Angular Gyrus	brain
11	chr4:53727400-53729600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr4:53727600-53728000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:53727600-53728000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
14	chr4:53727600-53728000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
15	chr4:53727600-53728000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
16	chr4:53727600-53728000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:53727600-53728000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:53727600-53728000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:53727600-53728000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:53727600-53728000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:53727600-53728000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
22	chr4:53727600-53728000	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr4:53727600-53728000	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr4:53727600-53728000	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr4:53727600-53728000	Flanking Active TSS	Ovary	ovary
26	chr4:53727600-53728000	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr4:53727600-53728200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:53727600-53728200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:53727600-53728200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:53727600-53728200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:53727600-53728200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:53727600-53728200	Flanking Active TSS	Fetal Brain Male	brain
33	chr4:53727600-53728200	Flanking Active TSS	Fetal Brain Female	brain
34	chr4:53727600-53728200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
35	chr4:53727600-53728400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
36	chr4:53727600-53728600	Bivalent/Poised TSS	Colonic Mucosa	Colon
37	chr4:53727600-53728800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
38	chr4:53727600-53728800	Active TSS	Brain Substantia Nigra	brain
39	chr4:53727600-53728800	Active TSS	Psoas Muscle	Psoas
40	chr4:53727600-53729200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr4:53727600-53729200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
42	chr4:53727600-53729200	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr4:53727600-53729600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr4:53727600-53729600	Active TSS	NHDF-Ad	bronchial
45	chr4:53727800-53728000	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:53727800-53728000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:53727800-53728000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:53727800-53728000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:53727800-53728000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr4:53727800-53728000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood

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