Variant report

Variant	rs35638196
Chromosome Location	chr4:54966104-54966105
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	ZBTB7A	chr4:54965818-54966467	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr4:54965542-54966365	ECC-1	luminal epithelium:	n/a	n/a
3	USF1	chr4:54966047-54966407	H1-hESC	embryonic stem cell:	n/a	chr4:54966277-54966290 chr4:54966279-54966288 chr4:54966280-54966289 chr4:54966279-54966288
4	CTBP2	chr4:54964983-54968272	H1-hESC	embryonic stem cell:	n/a	n/a
5	RUNX3	chr4:54965664-54966114	GM12878	blood:	n/a	chr4:54965879-54965894 chr4:54965877-54965892
6	TCF12	chr4:54965637-54966300	ECC-1	luminal epithelium:	n/a	n/a
7	EP300	chr4:54965546-54966258	ECC-1	luminal epithelium:	n/a	n/a
8	SUZ12	chr4:54964026-54970669	NT2-D1	testis:	n/a	n/a
9	BACH1	chr4:54965895-54966138	H1-hESC	embryonic stem cell:	n/a	n/a
10	SUZ12	chr4:54965302-54968257	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF12	chr4:54965624-54966260	ECC-1	luminal epithelium:	n/a	n/a
12	NFIC	chr4:54965455-54966280	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr4:54965717-54966137	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr4:54965847-54968503	H1-neurons	neurons:	n/a	n/a
15	USF1	chr4:54966084-54966440	SK-N-SH_RA	brain:	n/a	chr4:54966277-54966290 chr4:54966279-54966288 chr4:54966280-54966289 chr4:54966279-54966288
16	MAX	chr4:54965673-54966113	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54966084..54968498-chr4:54968560..54970883,2	MCF-7	breast:

Variant related genes	Relation type
GSX2	TF binding region
ENSG00000221219	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12500475	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12501838	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13114613	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13142462	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1346082	1.00[JPT][hapmap]
rs1364989	0.81[GIH][hapmap];0.91[MEX][hapmap]
rs34372785	0.82[EUR][1000 genomes]
rs35529982	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35818763	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41386153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817230	0.81[EUR][1000 genomes]
rs6842584	0.87[GIH][hapmap]
rs7695934	0.82[EUR][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	nsv879018	chr4:54714753-55030375	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1003167	chr4:54732051-55081905	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv537096	chr4:54732051-55081905	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv594202	chr4:54943432-55011123	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv594203	chr4:54960005-55030375	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54964800-54966200	Bivalent Enhancer	HSMMtube	muscle
2	chr4:54964800-54967800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:54965000-54966400	Enhancers	Spleen	Spleen
4	chr4:54965200-54966600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:54965200-54968000	Bivalent Enhancer	Placenta	Placenta
6	chr4:54965200-54968200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:54965200-54968200	Bivalent Enhancer	Lung	lung
8	chr4:54965400-54966200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
9	chr4:54965400-54966200	Bivalent Enhancer	HUVEC	blood vessel
10	chr4:54965400-54966200	Bivalent Enhancer	NH-A	brain
11	chr4:54965400-54966400	Bivalent Enhancer	Small Intestine	intestine
12	chr4:54965400-54966800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
13	chr4:54965400-54966800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
14	chr4:54965400-54967000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
15	chr4:54965400-54968000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
16	chr4:54965400-54968200	Bivalent Enhancer	Fetal Intestine Small	intestine
17	chr4:54965400-54968200	Bivalent Enhancer	Fetal Thymus	thymus
18	chr4:54965600-54966200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:54965600-54966200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
20	chr4:54965600-54966200	Bivalent Enhancer	Fetal Intestine Large	intestine
21	chr4:54965600-54966400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
22	chr4:54965600-54966400	Flanking Bivalent TSS/Enh	Right Ventricle	heart
23	chr4:54965600-54966600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:54965600-54966600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
25	chr4:54965600-54966800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr4:54965600-54966800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:54965600-54967000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
28	chr4:54965600-54967000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:54965600-54967200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:54965600-54967200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:54965600-54967200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:54965600-54967400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
33	chr4:54965600-54967600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr4:54965600-54967600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
35	chr4:54965600-54967600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
36	chr4:54965600-54968000	Bivalent Enhancer	Fetal Brain Male	brain
37	chr4:54965600-54968000	Bivalent Enhancer	Fetal Heart	heart
38	chr4:54965600-54968200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:54965600-54968200	Bivalent Enhancer	Esophagus	oesophagus
40	chr4:54965600-54968400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
41	chr4:54965800-54966200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:54965800-54966200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:54965800-54966200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
44	chr4:54965800-54966200	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr4:54965800-54966200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:54965800-54966200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:54965800-54966200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr4:54965800-54966200	Bivalent/Poised TSS	Thymus	Thymus
49	chr4:54965800-54966200	Bivalent Enhancer	NHEK	skin
50	chr4:54965800-54966200	Flanking Bivalent TSS/Enh	NHLF	lung

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