Variant report

Variant	rs2058147
Chromosome Location	chr4:15992486-15992487
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	POLR2A	chr4:15992091-15992941	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:15983233..15985275-chr4:15990629..15992884,2	MCF-7	breast:
2	chr4:15990358..15992506-chr4:15994289..15997209,3	K562	blood:
3	chr4:15992375..15993229-chr4:16010127..16010937,2	MCF-7	breast:
4	chr4:15986153..15988625-chr4:15990969..15992958,2	MCF-7	breast:

Variant related genes	Relation type
PROM1	TF binding region
ENSG00000007062	Chromatin interaction
ENSG00000251758	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10003313	0.83[EUR][1000 genomes]
rs11726546	1.00[CEU][hapmap]
rs16892760	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16892764	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2058146	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240683	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2240684	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302167	0.83[EUR][1000 genomes]
rs2677778	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28421727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4698132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4698437	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6449212	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9991714	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv461281	chr4:15984033-16001378	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv593770	chr4:15984033-16001378	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15964600-16031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:15968000-16002600	Weak transcription	Left Ventricle	heart
3	chr4:15968600-15993600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:15968800-15992600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:15969600-16011600	Weak transcription	Fetal Lung	lung
6	chr4:15971000-16008000	Weak transcription	Aorta	Aorta
7	chr4:15973200-15993800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:15976800-16002600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:15977000-16007400	Weak transcription	Gastric	stomach
10	chr4:15978000-15996800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:15978200-16003200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:15978800-16002800	Weak transcription	Right Ventricle	heart
13	chr4:15979400-16000400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:15979600-15996600	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr4:15979600-15998800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:15982200-16008200	Weak transcription	Brain Germinal Matrix	brain
17	chr4:15982600-15994400	Weak transcription	Fetal Intestine Large	intestine
18	chr4:15982800-16000200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:15983200-15992800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr4:15983200-15993000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:15983200-16000000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:15983400-15999800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:15983600-15992800	Strong transcription	Primary hematopoietic stem cells	blood
24	chr4:15983600-15992800	Strong transcription	Fetal Muscle Leg	muscle
25	chr4:15985400-15997000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:15987000-16003000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:15988400-16033800	Weak transcription	Pancreas	Pancrea
28	chr4:15988800-15992800	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr4:15988800-15995200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:15988800-15997000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:15989000-16008000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:15989000-16014400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:15989000-16024200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:15989800-16002200	Strong transcription	Fetal Stomach	stomach
35	chr4:15990000-15992800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:15990000-16015200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:15990600-15992600	Weak transcription	Fetal Kidney	kidney
38	chr4:15990600-15992800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:15990600-15996800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:15990800-15992800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr4:15990800-15993200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:15991000-15993200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:15991000-16029000	Weak transcription	Stomach Mucosa	stomach
44	chr4:15991200-15992600	Strong transcription	Colonic Mucosa	Colon
45	chr4:15991600-15993200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:15991600-15993800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:15991800-15992800	Strong transcription	Fetal Intestine Small	intestine
48	chr4:15991800-15996800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr4:15992000-15992800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr4:15992200-15992600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links