Variant report

Variant	rs10468902
Chromosome Location	chr18:29417515-29417516
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	chr18:29417503-29417705	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29415005..29417838-chr18:29671668..29674584,2	K562	blood:

Variant related genes	Relation type
TRAPPC8	TF binding region
ENSG00000265008	Chromatin interaction
ENSG00000134758	Chromatin interaction
ENSG00000238982	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1074636	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10853415	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853416	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11081718	1.00[JPT][hapmap]
rs11081720	0.95[JPT][hapmap]
rs11081729	0.95[JPT][hapmap]
rs11081730	0.84[EUR][1000 genomes]
rs11660557	0.95[JPT][hapmap]
rs11662341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11662697	0.95[JPT][hapmap]
rs11877256	1.00[JPT][hapmap]
rs12604640	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12604691	0.95[JPT][hapmap]
rs12606882	1.00[JPT][hapmap]
rs12606962	1.00[JPT][hapmap]
rs12607426	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12607786	0.95[JPT][hapmap]
rs12957331	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12969126	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1680643	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17741796	0.95[JPT][hapmap]
rs17742014	0.95[JPT][hapmap]
rs17742105	0.95[JPT][hapmap]
rs17804129	0.95[JPT][hapmap]
rs1786764	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1815822	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276144	0.95[JPT][hapmap]
rs35203717	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3737374	1.00[JPT][hapmap]
rs3826612	0.81[ASN][1000 genomes]
rs3865397	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4513172	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4545895	0.95[JPT][hapmap]
rs5011500	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs521491	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs549818	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs563247	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs639595	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506944	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6506945	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6506946	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs675570	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67874605	0.85[EUR][1000 genomes]
rs7228817	0.95[JPT][hapmap]
rs7229979	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7230326	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7231114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7234341	1.00[JPT][hapmap]
rs7234798	1.00[JPT][hapmap]
rs7239098	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7239951	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8084869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8088396	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8094542	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs930018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9966530	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1057229	chr18:29335175-29514265	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29394400-29418200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:29405600-29481800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:29406200-29518600	Weak transcription	Fetal Brain Male	brain
4	chr18:29406800-29431600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr18:29407400-29427400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr18:29407400-29429800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr18:29407400-29432000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:29407800-29431200	Weak transcription	Psoas Muscle	Psoas
9	chr18:29408000-29418200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr18:29408000-29460200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr18:29408400-29420800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:29408600-29420000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr18:29408600-29471800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr18:29408800-29419400	Strong transcription	Adipose Nuclei	Adipose
15	chr18:29408800-29419400	Strong transcription	Fetal Intestine Large	intestine
16	chr18:29409000-29418000	Weak transcription	Brain Germinal Matrix	brain
17	chr18:29409000-29420000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr18:29409000-29420000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr18:29409000-29439000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr18:29409000-29456600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr18:29409200-29419400	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr18:29409200-29419600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr18:29409600-29430000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr18:29409600-29430600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr18:29409800-29417800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr18:29409800-29432000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr18:29409800-29466600	Weak transcription	Gastric	stomach
28	chr18:29410400-29431400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr18:29410800-29418200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr18:29411000-29426200	Weak transcription	Esophagus	oesophagus
31	chr18:29412600-29420800	Strong transcription	Primary B cells from cord blood	blood
32	chr18:29412800-29418200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr18:29412800-29420200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr18:29412800-29420200	Strong transcription	Liver	Liver
35	chr18:29412800-29420200	Strong transcription	Dnd41	blood
36	chr18:29412800-29420400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr18:29413000-29419000	Strong transcription	Primary T cells from cord blood	blood
38	chr18:29413000-29419000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr18:29413000-29419000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr18:29413000-29419400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr18:29413000-29419400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr18:29413000-29419400	Strong transcription	Left Ventricle	heart
43	chr18:29413000-29420800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr18:29413000-29421000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr18:29413200-29419000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr18:29413200-29419000	Strong transcription	Fetal Muscle Leg	muscle
47	chr18:29413200-29419000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr18:29413200-29419400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr18:29413200-29420000	Strong transcription	Placenta	Placenta
50	chr18:29413200-29420600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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