Variant report

Variant	rs798217
Chromosome Location	chr1:94079927-94079928
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	POLR2A	chr1:94079799-94080412	HepG2	liver:	n/a	n/a
2	MXI1	chr1:94078695-94084544	SK-N-SH	brain:	n/a	chr1:94082665-94082680
3	POLR2A	chr1:94079181-94080536	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr1:94079927-94080502	T-47D	breast:	n/a	n/a
5	POLR2A	chr1:94079552-94079933	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr1:94079569-94081890	SK-N-SH	brain:	n/a	chr1:94080234-94080243 chr1:94081221-94081228
7	GATA3	chr1:94079918-94080501	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94048472..94052407-chr1:94077212..94082015,4	MCF-7	breast:
2	chr1:94079843..94082142-chr1:94311555..94313576,2	K562	blood:

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000137936	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000260464	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1772781	0.81[ASN][1000 genomes]
rs1772782	0.81[ASN][1000 genomes]
rs236273	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs236291	0.82[AMR][1000 genomes]
rs236301	0.80[AMR][1000 genomes]
rs236306	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236307	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236308	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236311	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236312	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs236343	0.90[AMR][1000 genomes]
rs236344	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs236345	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs368888	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs399649	0.81[ASN][1000 genomes]
rs423493	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798213	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs798218	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:94075400-94080000	Weak transcription	Fetal Thymus	thymus
3	chr1:94075600-94080600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:94075800-94081400	Strong transcription	Hela-S3	cervix
5	chr1:94076000-94080000	Strong transcription	NHEK	skin
6	chr1:94076000-94080800	Weak transcription	HUVEC	blood vessel
7	chr1:94076200-94080600	Genic enhancers	A549	lung
8	chr1:94077200-94099000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:94077600-94081200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr1:94077600-94084200	Enhancers	Fetal Brain Male	brain
11	chr1:94077800-94080000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:94078000-94080200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:94078000-94081000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:94078000-94081000	Weak transcription	Spleen	Spleen
15	chr1:94078000-94081000	Enhancers	HepG2	liver
16	chr1:94078200-94080600	Active TSS	Stomach Smooth Muscle	stomach
17	chr1:94078400-94080200	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:94078400-94084200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:94078600-94080200	Enhancers	Brain Anterior Caudate	brain
20	chr1:94078600-94081400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:94078600-94084400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:94078800-94080000	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr1:94078800-94080200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:94078800-94084200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:94078800-94084200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:94079000-94080000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:94079000-94080000	Flanking Active TSS	NHDF-Ad	bronchial
28	chr1:94079000-94080200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:94079000-94080400	Bivalent Enhancer	Fetal Heart	heart
30	chr1:94079000-94081400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:94079000-94084000	Enhancers	Brain Substantia Nigra	brain
32	chr1:94079200-94080000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:94079200-94080000	Flanking Active TSS	Osteobl	bone
34	chr1:94079200-94080200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
35	chr1:94079200-94080400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:94079200-94081200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr1:94079200-94081200	Transcr. at gene 5' and 3'	HSMM	muscle
38	chr1:94079200-94081800	Enhancers	Placenta Amnion	Placenta Amnion
39	chr1:94079200-94082800	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:94079200-94084000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr1:94079200-94084000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:94079200-94084200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:94079400-94080400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:94079400-94081600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:94079400-94083400	Enhancers	Esophagus	oesophagus
46	chr1:94079400-94084000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:94079400-94084200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:94079400-94084800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:94079400-94086800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:94079400-94088600	Enhancers	Fetal Intestine Large	intestine

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