Variant report

Variant	rs2280072
Chromosome Location	chr4:46995170-46995171
allele	C/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	ZNF143	chr4:46995156-46995276	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:46994742-46995958	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr4:46995129-46995927	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
GABRB1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10517171	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10517172	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10517173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10517174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10517175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11727160	0.81[ASN][1000 genomes]
rs11727163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11729000	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11731576	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16851647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859842	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2036940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762607	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3762608	0.82[ASN][1000 genomes]
rs3762610	0.81[AMR][1000 genomes]
rs3762611	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4695182	0.81[ASN][1000 genomes]
rs4695183	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57314699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59115556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59675437	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61409453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73813760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73813761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73813771	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73813772	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73813773	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470031	chr4:46982218-47006399	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:46993200-46995400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr4:46993400-46997400	Active TSS	Brain Angular Gyrus	brain
3	chr4:46993400-46997600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:46994000-46997400	Active TSS	Brain Anterior Caudate	brain
5	chr4:46994200-46996400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
6	chr4:46994400-46995200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:46994400-46995200	Enhancers	Esophagus	oesophagus
8	chr4:46994400-46995200	Active TSS	Left Ventricle	heart
9	chr4:46994400-46995600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr4:46994400-46995600	Enhancers	Pancreas	Pancrea
11	chr4:46994400-46996600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:46994400-46996600	Bivalent/Poised TSS	Fetal Brain Female	brain
13	chr4:46994600-46995200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:46994600-46995400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
15	chr4:46994600-46995400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
16	chr4:46994600-46995600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr4:46994600-46995800	Bivalent/Poised TSS	Right Ventricle	heart
18	chr4:46994600-46996600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr4:46994800-46995200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
20	chr4:46994800-46995200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:46994800-46995200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:46994800-46995200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
23	chr4:46994800-46995200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
24	chr4:46994800-46995800	Bivalent Enhancer	Placenta	Placenta
25	chr4:46994800-46996000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:46994800-46996600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
27	chr4:46994800-46996600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr4:46994800-46996600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
29	chr4:46994800-46996600	Active TSS	Fetal Heart	heart
30	chr4:46994800-46997000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr4:46995000-46995200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:46995000-46995200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr4:46995000-46995200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:46995000-46995200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
35	chr4:46995000-46995200	Bivalent Enhancer	Fetal Stomach	stomach
36	chr4:46995000-46995200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
37	chr4:46995000-46995400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
38	chr4:46995000-46995600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:46995000-46995600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr4:46995000-46995600	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr4:46995000-46995800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr4:46995000-46995800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
43	chr4:46995000-46996000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
44	chr4:46995000-46996000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:46995000-46996200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:46995000-46996200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
47	chr4:46995000-46996400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:46995000-46996400	Bivalent/Poised TSS	Colonic Mucosa	Colon
49	chr4:46995000-46996400	Flanking Bivalent TSS/Enh	NH-A	brain
50	chr4:46995000-46996600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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