Variant report

Variant	rs59416609
Chromosome Location	chr22:31840474-31840475
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	POLR2A	chr22:31840434-31840753	GM12878	blood:	n/a	n/a
2	POLR2A	chr22:31834979-31841892	K562	blood:	n/a	n/a
3	POLR2A	chr22:31839680-31840522	HepG2	liver:	n/a	n/a
4	POLR2A	chr22:31840317-31841329	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	22:31836635-31847259..22:31936958-31958600	GM12878	blood:
2	22:31836635-31847259..22:32529813-32538538	K562	blood:
3	chr22:31834066..31836776-chr22:31838775..31841114,2	K562	blood:
4	chr22:31839629..31841921-chr22:31886106..31888362,2	K562	blood:
5	22:31836635-31847259..22:32284948-32287956	Hela-S3	cervix:

Variant related genes	Relation type
EIF4ENIF1	TF binding region
ENSG00000184708	Chromatin interaction
ENSG00000214093	Chromatin interaction
ENSG00000239674	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000227813	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10483159	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11089501	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11089502	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11089503	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11089504	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12165685	1.00[EUR][1000 genomes]
rs12168242	1.00[EUR][1000 genomes]
rs12169794	0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12484188	0.89[ASN][1000 genomes]
rs12484233	0.89[ASN][1000 genomes]
rs12484646	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12484775	1.00[EUR][1000 genomes]
rs12484858	0.89[ASN][1000 genomes]
rs12484966	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12485176	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12485177	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17820958	1.00[EUR][1000 genomes]
rs17821132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1859677	1.00[EUR][1000 genomes]
rs1968024	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2073856	1.00[EUR][1000 genomes]
rs2073859	1.00[EUR][1000 genomes]
rs2073860	1.00[EUR][1000 genomes]
rs2073861	1.00[EUR][1000 genomes]
rs2158779	1.00[EUR][1000 genomes]
rs2240424	1.00[EUR][1000 genomes]
rs2267168	1.00[EUR][1000 genomes]
rs2273248	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2283882	1.00[EUR][1000 genomes]
rs2295240	0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2295241	0.89[ASN][1000 genomes]
rs28678535	1.00[EUR][1000 genomes]
rs28872513	1.00[EUR][1000 genomes]
rs35208364	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3747153	1.00[EUR][1000 genomes]
rs3747154	1.00[EUR][1000 genomes]
rs3747155	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788434	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3788435	0.89[ASN][1000 genomes]
rs5749233	1.00[EUR][1000 genomes]
rs5749236	1.00[EUR][1000 genomes]
rs5749239	1.00[EUR][1000 genomes]
rs5749240	1.00[EUR][1000 genomes]
rs5749247	1.00[EUR][1000 genomes]
rs5749252	1.00[EUR][1000 genomes]
rs5749255	1.00[EUR][1000 genomes]
rs5749258	1.00[EUR][1000 genomes]
rs5749262	1.00[EUR][1000 genomes]
rs5749263	1.00[EUR][1000 genomes]
rs5753506	1.00[EUR][1000 genomes]
rs5753509	1.00[EUR][1000 genomes]
rs5753511	1.00[EUR][1000 genomes]
rs5753512	1.00[EUR][1000 genomes]
rs5753513	1.00[EUR][1000 genomes]
rs5753516	1.00[EUR][1000 genomes]
rs5753519	1.00[EUR][1000 genomes]
rs5753525	1.00[EUR][1000 genomes]
rs5753526	1.00[EUR][1000 genomes]
rs5753527	1.00[EUR][1000 genomes]
rs5753529	1.00[EUR][1000 genomes]
rs5753532	1.00[EUR][1000 genomes]
rs5753534	1.00[EUR][1000 genomes]
rs5753535	1.00[EUR][1000 genomes]
rs5753540	1.00[EUR][1000 genomes]
rs5753555	1.00[EUR][1000 genomes]
rs5753556	1.00[EUR][1000 genomes]
rs5753566	1.00[EUR][1000 genomes]
rs5753569	1.00[EUR][1000 genomes]
rs5753571	1.00[EUR][1000 genomes]
rs5753572	1.00[EUR][1000 genomes]
rs58856347	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58915086	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7292620	1.00[EUR][1000 genomes]
rs73396257	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9619178	1.00[EUR][1000 genomes]
rs9621215	1.00[EUR][1000 genomes]
rs9621220	1.00[EUR][1000 genomes]
rs9621226	1.00[EUR][1000 genomes]
rs9621236	1.00[EUR][1000 genomes]
rs9621247	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9621252	1.00[EUR][1000 genomes]
rs9621261	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9621263	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9621264	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9621265	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9621270	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][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	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:31797200-31845400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr22:31797200-31846200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr22:31797200-31846400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr22:31797200-31860600	Strong transcription	Fetal Stomach	stomach
7	chr22:31797400-31846800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr22:31797800-31844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr22:31797800-31846800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr22:31799000-31845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr22:31799200-31846600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr22:31803600-31844600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr22:31804600-31847000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr22:31805000-31844800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr22:31805600-31844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr22:31806800-31842400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr22:31812000-31842000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr22:31813600-31845000	Strong transcription	Fetal Thymus	thymus
19	chr22:31814000-31841200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr22:31814000-31846400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr22:31814200-31846800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr22:31814400-31845600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr22:31814400-31845800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr22:31814400-31846800	Strong transcription	Fetal Intestine Large	intestine
25	chr22:31814600-31841400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr22:31814600-31841600	Strong transcription	Lung	lung
27	chr22:31814800-31844600	Strong transcription	Thymus	Thymus
28	chr22:31814800-31846600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr22:31815000-31841400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr22:31815000-31844600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr22:31815000-31846600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:31815000-31846800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr22:31815000-31868200	Strong transcription	Dnd41	blood
34	chr22:31815000-31883400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr22:31815400-31844400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr22:31815400-31844400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr22:31815400-31846200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr22:31815400-31846600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:31815400-31846600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr22:31815600-31844200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr22:31815800-31841600	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr22:31816200-31842200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr22:31821000-31844600	Strong transcription	Primary B cells from cord blood	blood
44	chr22:31821000-31845000	Strong transcription	Primary T cells from cord blood	blood
45	chr22:31821200-31844600	Strong transcription	Fetal Brain Female	brain
46	chr22:31822200-31846600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr22:31822400-31859800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr22:31823600-31884600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr22:31825600-31841800	Strong transcription	Gastric	stomach
50	chr22:31825800-31841800	Strong transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links