Variant report

Variant	rs28407704
Chromosome Location	chr8:48571694-48571695
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	chr8:48571671-48571794	ProgFib	skin:	n/a	n/a
2	MAZ	chr8:48571580-48571716	K562	blood:	n/a	n/a
3	NR3C1	chr8:48571530-48572664	A549	lung:	n/a	chr8:48572086-48572100 chr8:48572085-48572101 chr8:48572080-48572106 chr8:48572085-48572101 chr8:48572086-48572100 chr8:48572080-48572106 chr8:48572085-48572101 chr8:48572084-48572102 chr8:48572080-48572106 chr8:48572083-48572104 chr8:48572085-48572101 chr8:48572080-48572106 chr8:48572080-48572106
4	MAZ	chr8:48571457-48572776	IMR90	lung:	n/a	n/a
5	MAX	chr8:48571532-48573195	HepG2	liver:	n/a	n/a
6	MAX	chr8:48571612-48571865	K562	blood:	n/a	n/a
7	FOXA2	chr8:48571637-48572897	HepG2	liver:	n/a	n/a
8	MXI1	chr8:48571641-48572771	IMR90	lung:	n/a	n/a
9	RCOR1	chr8:48571534-48572722	K562	blood:	n/a	n/a
10	HCFC1	chr8:48571649-48572656	K562	blood:	n/a	n/a
11	POLR2A	chr8:48571547-48573557	MCF10A-Er-Src	breast:	n/a	n/a
12	ZNF384	chr8:48571286-48572704	K562	blood:	n/a	n/a
13	POLR2A	chr8:48571524-48573502	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr8:48571675-48572873	U87	brain:	n/a	n/a
15	NR3C1	chr8:48571526-48571896	A549	lung:	n/a	n/a
16	POLR2A	chr8:48571634-48571806	MCF-7	breast:	n/a	n/a
17	POLR2A	chr8:48571386-48572785	K562	blood:	n/a	n/a
18	TEAD4	chr8:48571663-48572781	K562	blood:	n/a	n/a
19	POLR2A	chr8:48571554-48573598	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:48570759..48574488-chr8:48583570..48586841,4	K562	blood:
2	chr8:48571104..48575817-chr8:48648052..48653139,6	K562	blood:
3	chr8:48571020..48572523-chr8:48650365..48652333,2	MCF-7	breast:

Variant related genes	Relation type
SPIDR	TF binding region
ENSG00000221869	Chromatin interaction
ENSG00000164808	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10093950	0.88[AFR][1000 genomes]
rs10099656	0.88[AFR][1000 genomes]
rs10102782	0.88[AFR][1000 genomes]
rs10104074	0.92[AFR][1000 genomes]
rs10106803	0.80[AFR][1000 genomes]
rs10108990	0.82[AFR][1000 genomes]
rs10110049	0.82[AFR][1000 genomes]
rs10111963	0.88[AFR][1000 genomes]
rs11987727	0.88[AFR][1000 genomes]
rs11997023	0.84[AFR][1000 genomes]
rs28366397	0.88[AFR][1000 genomes]
rs28439682	0.88[AFR][1000 genomes]
rs28583978	0.82[AFR][1000 genomes]
rs28603312	0.84[AFR][1000 genomes]
rs28683713	0.82[AFR][1000 genomes]
rs6980675	0.84[AFR][1000 genomes]
rs7003614	0.82[AFR][1000 genomes]
rs7010172	0.82[AFR][1000 genomes]
rs7014936	0.82[AFR][1000 genomes]
rs73677550	0.82[AFR][1000 genomes]
rs7823419	0.88[AFR][1000 genomes]
rs8178253	0.80[AFR][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	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1027043	chr8:48444306-48637900	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv539596	chr8:48444306-48637900	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1803608	chr8:48506628-48874811	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48519400-48573600	Weak transcription	Primary T cells from cord blood	blood
2	chr8:48523800-48572200	Weak transcription	Primary B cells from cord blood	blood
3	chr8:48555400-48572200	Weak transcription	Fetal Intestine Small	intestine
4	chr8:48555400-48573800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr8:48565600-48574400	Weak transcription	Aorta	Aorta
6	chr8:48565800-48571800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:48569600-48572200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr8:48570400-48571800	Enhancers	Lung	lung
9	chr8:48570400-48573000	Weak transcription	Small Intestine	intestine
10	chr8:48570400-48575000	Enhancers	Pancreas	Pancrea
11	chr8:48570600-48572600	Weak transcription	Gastric	stomach
12	chr8:48570800-48572400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:48571000-48572000	Enhancers	Right Atrium	heart
14	chr8:48571000-48572200	Enhancers	Left Ventricle	heart
15	chr8:48571000-48572200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr8:48571200-48571800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr8:48571200-48571800	Enhancers	Fetal Stomach	stomach
18	chr8:48571200-48572000	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr8:48571200-48572000	Enhancers	Ovary	ovary
20	chr8:48571200-48572000	Enhancers	Right Ventricle	heart
21	chr8:48571200-48572200	Enhancers	Fetal Muscle Trunk	muscle
22	chr8:48571200-48572200	Enhancers	Placenta	Placenta
23	chr8:48571200-48572600	Active TSS	Rectal Smooth Muscle	rectum
24	chr8:48571200-48573200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr8:48571200-48574800	Enhancers	Brain Angular Gyrus	brain
26	chr8:48571200-48574800	Enhancers	Psoas Muscle	Psoas
27	chr8:48571400-48571800	Enhancers	Brain Substantia Nigra	brain
28	chr8:48571400-48571800	Enhancers	Fetal Muscle Leg	muscle
29	chr8:48571400-48572000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr8:48571400-48572000	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr8:48571400-48572600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr8:48571400-48573600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr8:48571600-48571800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr8:48571600-48571800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:48571600-48571800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr8:48571600-48571800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr8:48571600-48571800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr8:48571600-48571800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr8:48571600-48571800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr8:48571600-48571800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:48571600-48571800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr8:48571600-48571800	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr8:48571600-48571800	Flanking Active TSS	Liver	Liver
44	chr8:48571600-48571800	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr8:48571600-48571800	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr8:48571600-48571800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr8:48571600-48571800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr8:48571600-48571800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
49	chr8:48571600-48571800	Enhancers	Esophagus	oesophagus
50	chr8:48571600-48571800	Enhancers	Fetal Thymus	thymus

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