Variant report

Variant	rs3755901
Chromosome Location	chr4:57775996-57775997
allele	A/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	POLR2A	chr4:57775876-57776063	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr4:57774532-57776163	Hela-S3	cervix:	n/a	n/a
3	WRNIP1	chr4:57775621-57776091	GM12878	blood:	n/a	n/a
4	YY1	chr4:57775779-57776126	GM12892	blood:	n/a	n/a
5	YY1	chr4:57775867-57776110	GM12878	blood:	n/a	n/a
6	MXI1	chr4:57773345-57776166	IMR90	lung:	n/a	n/a
7	YY1	chr4:57775754-57776150	ECC-1	luminal epithelium:	n/a	n/a
8	CHD1	chr4:57774719-57776234	GM12878	blood:	n/a	n/a
9	TEAD4	chr4:57775231-57776110	K562	blood:	n/a	n/a
10	YY1	chr4:57775817-57776124	GM12878	blood:	n/a	n/a
11	UBTF	chr4:57773819-57776233	K562	blood:	n/a	n/a
12	POLR2A	chr4:57775094-57776108	Hela-S3	cervix:	n/a	n/a
13	YY1	chr4:57775098-57776077	H1-hESC	embryonic stem cell:	n/a	n/a
14	EP300	chr4:57775390-57775997	GM12878	blood:	n/a	n/a
15	TBP	chr4:57775162-57776074	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr4:57775840-57776046	A549	lung:	n/a	n/a
17	MYC	chr4:57773776-57776081	NB4	blood:	n/a	n/a
18	IRF1	chr4:57774897-57776326	K562	blood:	n/a	n/a
19	POLR2A	chr4:57775811-57776056	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:57774039-57776016	HepG2	liver:	n/a	n/a
21	YY1	chr4:57775852-57776134	GM12891	blood:	n/a	n/a
22	YY1	chr4:57775190-57776062	H1-hESC	embryonic stem cell:	n/a	n/a
23	TBP	chr4:57775421-57776110	Hela-S3	cervix:	n/a	n/a
24	YY1	chr4:57775838-57776094	K562	blood:	n/a	n/a
25	YY1	chr4:57775146-57776134	SK-N-SH_RA	brain:	n/a	n/a
26	TBL1XR1	chr4:57775599-57775999	GM12878	blood:	n/a	n/a
27	TBP	chr4:57773881-57776083	K562	blood:	n/a	n/a
28	POLR2A	chr4:57773848-57776306	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr4:57775825-57776158	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr4:57773881-57776058	Hela-S3	cervix:	n/a	n/a
31	REST	chr4:57773798-57776230	HL-60	blood:	n/a	chr4:57774480-57774489 chr4:57773900-57773913 chr4:57774581-57774591 chr4:57774720-57774734 chr4:57774122-57774135 chr4:57774480-57774493 chr4:57774118-57774138
32	MXI1	chr4:57773813-57776164	GM12878	blood:	n/a	n/a
33	TAF1	chr4:57775847-57776111	H1-hESC	embryonic stem cell:	n/a	n/a
34	STAT3	chr4:57775840-57775998	GM12878	blood:	n/a	n/a
35	SIN3A	chr4:57773045-57776084	H1-hESC	embryonic stem cell:	n/a	chr4:57774969-57774978 chr4:57774574-57774587 chr4:57774972-57774985 chr4:57774938-57774951 chr4:57774480-57774493 chr4:57774388-57774401 chr4:57774851-57774862
36	E2F4	chr4:57775924-57776354	MCF10A-Er-Src	breast:	n/a	chr4:57776121-57776130
37	POLR2A	chr4:57774751-57776410	GM12891	blood:	n/a	n/a
38	POLR2A	chr4:57775818-57776076	H1-hESC	embryonic stem cell:	n/a	n/a
39	CHD1	chr4:57774494-57776306	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr4:57773868-57776085	H1-hESC	embryonic stem cell:	n/a	n/a
41	YY1	chr4:57775829-57776077	GM12892	blood:	n/a	n/a
42	YY1	chr4:57775809-57776083	HepG2	liver:	n/a	n/a
43	YY1	chr4:57775206-57776165	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr4:57774920-57776106	PBDE	blood:	n/a	n/a
45	MAZ	chr4:57775801-57776102	GM12878	blood:	n/a	n/a
46	POLR2A	chr4:57773896-57776043	GM18505	blood:	n/a	n/a
47	YY1	chr4:57775224-57776155	SK-N-SH_RA	brain:	n/a	n/a
48	BRCA1	chr4:57775259-57776137	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57772839..57777394-chr4:57841397..57848240,17	K562	blood:
2	chr4:57301355..57303854-chr4:57773620..57776020,4	MCF-7	breast:
3	chr4:57771688..57776264-chr4:57841866..57845328,7	MCF-7	breast:
4	chr4:57774412..57776864-chr4:57776976..57782053,6	K562	blood:
5	chr4:57299951..57301849-chr4:57773604..57776000,3	K562	blood:
6	chr4:57252189..57254981-chr4:57775973..57777493,2	MCF-7	breast:
7	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:

Variant related genes	Relation type
REST	TF binding region
ENSG00000128059	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000084092	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000084093	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10002090	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10026915	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs11573061	0.87[CEU][hapmap]
rs11573112	0.87[YRI][hapmap]
rs11573113	1.00[YRI][hapmap]
rs11935933	0.92[EUR][1000 genomes]
rs11942607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1277296	0.82[CEU][hapmap]
rs13146782	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs17182939	0.87[CEU][hapmap]
rs17828496	0.80[EUR][1000 genomes]
rs1980095	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227902	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2227903	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271806	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2271807	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2276896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs28451372	1.00[ASN][1000 genomes]
rs28472594	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28520821	0.80[EUR][1000 genomes]
rs3755904	1.00[YRI][hapmap]
rs3775083	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs41344750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs55734441	0.80[EUR][1000 genomes]
rs6554404	0.82[CEU][hapmap]
rs6837593	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs73242603	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73242618	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73242619	0.83[EUR][1000 genomes]
rs73242620	0.80[EUR][1000 genomes]
rs73242621	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs73242622	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs73242623	0.80[EUR][1000 genomes]
rs73242625	0.80[EUR][1000 genomes]
rs7654665	0.82[CEU][hapmap]
rs7673980	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs781552	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs781557	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs781559	0.81[AMR][1000 genomes];0.94[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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv822562	chr4:57768655-57779715	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3374947	chr4:57773220-57776168	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57772800-57776200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:57773000-57776000	Active TSS	Rectal Smooth Muscle	rectum
3	chr4:57773200-57776000	Active TSS	A549	lung
4	chr4:57773200-57776000	Active TSS	HMEC	breast
5	chr4:57773200-57776200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:57773200-57776200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:57773200-57776400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr4:57773200-57776600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr4:57773200-57776600	Active TSS	Aorta	Aorta
10	chr4:57773200-57776800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:57773400-57776000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:57773400-57776000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:57773400-57776000	Active TSS	Duodenum Mucosa	Duodenum
14	chr4:57773400-57776200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:57773400-57776200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:57773400-57776200	Active TSS	Brain Anterior Caudate	brain
17	chr4:57773400-57776200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr4:57773400-57776200	Active TSS	Ovary	ovary
19	chr4:57773400-57776600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr4:57773400-57776800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:57773400-57776800	Active TSS	Psoas Muscle	Psoas
22	chr4:57773600-57776000	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr4:57773600-57776000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:57773600-57776000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:57773600-57776000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr4:57773600-57776000	Active TSS	Fetal Lung	lung
27	chr4:57773600-57776000	Active TSS	Left Ventricle	heart
28	chr4:57773600-57776000	Active TSS	Pancreas	Pancrea
29	chr4:57773600-57776000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr4:57773600-57776200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:57773600-57776200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:57773600-57776200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:57773600-57776200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:57773600-57776200	Active TSS	Colon Smooth Muscle	Colon
35	chr4:57773600-57776200	Active TSS	Fetal Muscle Trunk	muscle
36	chr4:57773600-57776200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr4:57773600-57776200	Active TSS	Thymus	Thymus
38	chr4:57773600-57776400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:57773600-57776400	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr4:57773600-57776400	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr4:57773600-57776400	Active TSS	Fetal Muscle Leg	muscle
42	chr4:57773600-57776400	Active TSS	Fetal Stomach	stomach
43	chr4:57773600-57776400	Active TSS	Right Atrium	heart
44	chr4:57773600-57776400	Active TSS	Right Ventricle	heart
45	chr4:57773600-57776400	Active TSS	Stomach Smooth Muscle	stomach
46	chr4:57773600-57776400	Active TSS	NHLF	lung
47	chr4:57773600-57776600	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr4:57773600-57776600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:57773600-57776600	Active TSS	Fetal Intestine Large	intestine
50	chr4:57773600-57776600	Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links