Variant report

Variant	rs28399556
Chromosome Location	chr8:95906034-95906035
allele	G/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	CTCF	chr8:95905940-95906090	GM12872	blood:	n/a	chr8:95905978-95905991
2	PRDM1	chr8:95905777-95906305	Hela-S3	cervix:	n/a	chr8:95906006-95906020 chr8:95906005-95906020
3	CTCF	chr8:95905900-95906050	GM12875	blood:	n/a	chr8:95905978-95905991
4	CTCF	chr8:95905900-95906050	GM06990	blood:	n/a	chr8:95905978-95905991
5	CTCF	chr8:95905900-95906050	BE2_C	brain:	n/a	chr8:95905978-95905991
6	CTCF	chr8:95905900-95906050	MCF-7	breast:	n/a	chr8:95905978-95905991
7	CTCF	chr8:95905928-95906054	K562	blood:	n/a	chr8:95905978-95905991
8	CTCF	chr8:95905920-95906070	MCF-7	breast:	n/a	chr8:95905978-95905991
9	CTCF	chr8:95905900-95906050	GM12864	blood:	n/a	chr8:95905978-95905991
10	SIN3A	chr8:95905721-95909315	H1-hESC	embryonic stem cell:	n/a	chr8:95908237-95908248 chr8:95907214-95907227 chr8:95906806-95906819 chr8:95906987-95906998 chr8:95908097-95908108 chr8:95908761-95908769
11	CTCF	chr8:95905940-95906090	GM12867	blood:	n/a	chr8:95905978-95905991
12	HCFC1	chr8:95905561-95909556	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr8:95905900-95906050	GM12872	blood:	n/a	chr8:95905978-95905991
14	SIN3AK20	chr8:95905630-95909476	MCF-7	breast:	n/a	n/a
15	CTCF	chr8:95905920-95906070	GM12873	blood:	n/a	chr8:95905978-95905991
16	CTCF	chr8:95905900-95906050	AG10803	skin:	n/a	chr8:95905978-95905991
17	GATA1	chr8:95905339-95906912	PBDE	blood:	n/a	chr8:95905684-95905692
18	CTCF	chr8:95905920-95906070	HMF	breast:	n/a	chr8:95905978-95905991
19	RAD21	chr8:95905836-95906123	Hela-S3	cervix:	n/a	n/a
20	RAD21	chr8:95905846-95906122	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr8:95905824-95906123	K562	blood:	n/a	chr8:95905978-95905991
22	CTCF	chr8:95905900-95906050	GM12871	blood:	n/a	chr8:95905978-95905991
23	CTCF	chr8:95905960-95906110	NHDF-neo	bronchial:	n/a	chr8:95905978-95905991
24	CTCF	chr8:95905900-95906050	GM12866	blood:	n/a	chr8:95905978-95905991
25	CTCF	chr8:95905900-95906050	AG09319	gingival:	n/a	chr8:95905978-95905991
26	CTCF	chr8:95905923-95906046	MCF-7	breast:	n/a	chr8:95905978-95905991
27	CTCF	chr8:95905937-95906036	MCF-7	breast:	n/a	chr8:95905978-95905991
28	CTCF	chr8:95905900-95906050	Hela-S3	cervix:	n/a	chr8:95905978-95905991
29	POLR2A	chr8:95905613-95909393	SK-N-MC	brain:	n/a	n/a
30	CTCF	chr8:95905940-95906090	GM12871	blood:	n/a	chr8:95905978-95905991
31	CTCF	chr8:95905920-95906070	BE2_C	brain:	n/a	chr8:95905978-95905991
32	JUN	chr8:95905679-95909615	K562	blood:	n/a	chr8:95907471-95907480 chr8:95907973-95907982 chr8:95906827-95906836
33	CTCF	chr8:95905940-95906090	GM12864	blood:	n/a	chr8:95905978-95905991
34	CTCF	chr8:95905900-95906050	HL-60	blood:	n/a	chr8:95905978-95905991
35	MAX	chr8:95905803-95906083	NB4	blood:	n/a	n/a
36	CTCF	chr8:95905918-95906044	GM12878	blood:	n/a	chr8:95905978-95905991
37	CTCF	chr8:95905900-95906050	HRPEpiC	eye:	n/a	chr8:95905978-95905991
38	CTCF	chr8:95905920-95906070	GM06990	blood:	n/a	chr8:95905978-95905991
39	CTCF	chr8:95905960-95906110	GM12873	blood:	n/a	chr8:95905978-95905991
40	CTCF	chr8:95906020-95906170	GM12870	blood:	n/a	n/a
41	CTCF	chr8:95905908-95906055	Hela-S3	cervix:	n/a	chr8:95905978-95905991
42	CTCF	chr8:95905863-95906153	GM12878	blood:	n/a	chr8:95905978-95905991
43	CTCF	chr8:95905920-95906070	GM12865	blood:	n/a	chr8:95905978-95905991
44	MXI1	chr8:95905609-95910254	SK-N-SH	brain:	n/a	n/a
45	CTCF	chr8:95905920-95906070	GM12867	blood:	n/a	chr8:95905978-95905991
46	E2F4	chr8:95905859-95906059	MCF10A-Er-Src	breast:	n/a	n/a
47	RAD21	chr8:95905742-95906178	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:95905635..95908338-chr8:95917636..95919532,2	MCF-7	breast:
2	chr8:95833645..95837522-chr8:95905761..95911691,14	MCF-7	breast:
3	chr8:95905969..95907155-chr8:96036661..96037534,3	MCF-7	breast:
4	chr8:95833775..95836713-chr8:95905419..95909134,3	MCF-7	breast:
5	chr8:95905045..95910108-chr8:95959761..95963234,8	MCF-7	breast:
6	chr8:95905055..95911257-chr8:96032486..96039313,18	MCF-7	breast:

Variant related genes	Relation type
NDUFAF6	TF binding region
CCNE2	TF binding region
ENSG00000164938	Chromatin interaction
ENSG00000238791	Chromatin interaction
ENSG00000156170	Chromatin interaction
ENSG00000164941	Chromatin interaction
ENSG00000253878	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2305466	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28399561	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4269509	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57099803	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7844910	0.89[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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv891203	chr8:95883232-95948202	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv891204	chr8:95883232-95965135	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95876200-95906600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:95879200-95906600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:95882200-95906600	Weak transcription	Gastric	stomach
4	chr8:95886000-95906400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:95887600-95906200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:95888200-95906600	Weak transcription	Ovary	ovary
7	chr8:95890000-95906200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr8:95890200-95906600	Weak transcription	Lung	lung
9	chr8:95890600-95906800	Weak transcription	Aorta	Aorta
10	chr8:95891000-95906600	Weak transcription	Left Ventricle	heart
11	chr8:95892400-95906400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr8:95894000-95906200	Weak transcription	Fetal Kidney	kidney
13	chr8:95894800-95906400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr8:95895200-95906200	Weak transcription	Fetal Intestine Large	intestine
15	chr8:95896200-95906400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr8:95896200-95906600	Weak transcription	HSMMtube	muscle
17	chr8:95898800-95906600	Weak transcription	Right Ventricle	heart
18	chr8:95899200-95906200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:95899600-95906200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr8:95899600-95906200	Weak transcription	Fetal Intestine Small	intestine
21	chr8:95902000-95906200	Weak transcription	NH-A	brain
22	chr8:95904800-95906200	Enhancers	Fetal Heart	heart
23	chr8:95905200-95906400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr8:95905400-95906200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr8:95905400-95906200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr8:95905400-95906400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr8:95905400-95906400	Active TSS	Brain Cingulate Gyrus	brain
28	chr8:95905400-95906400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr8:95905400-95906600	Flanking Active TSS	Hela-S3	cervix
30	chr8:95905400-95907400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr8:95905400-95907400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr8:95905600-95906200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr8:95905600-95906200	Active TSS	Brain Hippocampus Middle	brain
34	chr8:95905600-95906200	Active TSS	Fetal Muscle Trunk	muscle
35	chr8:95905600-95906200	Enhancers	K562	blood
36	chr8:95905600-95906400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:95905600-95906400	Enhancers	Primary B cells from peripheral blood	blood
38	chr8:95905600-95906400	Active TSS	Primary T cells from cord blood	blood
39	chr8:95905600-95906400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr8:95905600-95906400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr8:95905600-95906400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr8:95905600-95906400	Active TSS	Brain Angular Gyrus	brain
43	chr8:95905600-95906400	Active TSS	Brain Anterior Caudate	brain
44	chr8:95905600-95906400	Enhancers	Placenta	Placenta
45	chr8:95905600-95906400	Active TSS	NHLF	lung
46	chr8:95905600-95906600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr8:95905600-95906600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr8:95905600-95906600	Enhancers	Pancreas	Pancrea
49	chr8:95905600-95906600	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr8:95905600-95906600	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links