Variant report

Variant	rs874250
Chromosome Location	chr18:9119156-9119157
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	chr18:9119048-9119158	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9102444..9104093-chr18:9117938..9120762,2	MCF-7	breast:
2	chr18:9117343..9120126-chr18:9132921..9134783,2	K562	blood:
3	chr18:9117343..9119164-chr18:9132921..9135865,2	K562	blood:

Variant related genes	Relation type
NDUFV2	TF binding region
ENSG00000263847	TF binding region
ENSG00000178127	Chromatin interaction
ENSG00000265257	Chromatin interaction
ENSG00000266053	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10451358	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs11081462	0.90[EUR][1000 genomes]
rs11081465	0.89[CEU][hapmap]
rs11081466	0.81[AFR][1000 genomes]
rs1156044	0.91[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap]
rs11660603	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12954031	0.80[AFR][1000 genomes]
rs1396740	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1443596	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap]
rs1472944	0.81[ASN][1000 genomes]
rs17413793	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs1785560	0.91[CEU][hapmap]
rs1893198	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs2028656	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2155707	0.82[CHB][hapmap]
rs2276095	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078337	0.86[CHB][hapmap]
rs4130178	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4131992	0.86[CHB][hapmap]
rs4148964	0.91[ASN][1000 genomes]
rs4148965	0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4318275	0.83[YRI][hapmap]
rs4603624	0.82[CHB][hapmap]
rs4797356	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs4797361	0.82[CHB][hapmap]
rs4798771	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4798772	0.85[CHD][hapmap]
rs4798776	0.90[CHB][hapmap]
rs4798778	0.84[CHD][hapmap]
rs4798785	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs4798786	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs4798789	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs4798790	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs4798791	0.89[CHD][hapmap]
rs6506644	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6506648	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7228251	0.90[CHD][hapmap]
rs7229883	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs7231452	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs7235514	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7240452	0.81[AFR][1000 genomes]
rs7505266	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7506291	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs8083078	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8084822	0.91[CEU][hapmap];0.81[CHD][hapmap]
rs8089693	0.90[CHD][hapmap]
rs8092135	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8092613	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs8092878	0.91[CEU][hapmap]
rs906807	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9646498	0.83[AFR][1000 genomes]
rs9652952	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs977581	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs9945360	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs9946468	0.86[CHB][hapmap]
rs9946695	0.90[CHD][hapmap]
rs9946838	0.83[AFR][1000 genomes]
rs9948560	0.94[CHB][hapmap]
rs9960129	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs998171	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]

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	nsv1064883	chr18:8709670-9133224	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv431971	chr18:9081185-9326852	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1056258	chr18:9094498-9181498	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv909364	chr18:9114096-9186684	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 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	chr18:9104400-9130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:9106200-9123200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr18:9107000-9135200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:9107400-9135400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:9107600-9123200	Weak transcription	Thymus	Thymus
6	chr18:9107800-9134600	Weak transcription	Fetal Brain Male	brain
7	chr18:9108200-9123000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:9108200-9127200	Weak transcription	Fetal Brain Female	brain
9	chr18:9109600-9123200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:9111200-9125400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr18:9111600-9126800	Weak transcription	Colonic Mucosa	Colon
12	chr18:9111800-9123400	Weak transcription	Fetal Stomach	stomach
13	chr18:9113000-9119800	Enhancers	Brain Hippocampus Middle	brain
14	chr18:9114000-9119600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr18:9114000-9121000	Weak transcription	Fetal Muscle Leg	muscle
16	chr18:9114000-9123200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:9114000-9123400	Weak transcription	Fetal Intestine Small	intestine
18	chr18:9114000-9127400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr18:9114000-9130800	Weak transcription	Ovary	ovary
20	chr18:9115400-9134600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr18:9115600-9119600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr18:9115600-9119800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:9115800-9134800	Strong transcription	Dnd41	blood
24	chr18:9116000-9119600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr18:9116600-9119200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr18:9116600-9119400	Enhancers	Primary hematopoietic stem cells	blood
27	chr18:9116600-9119400	Enhancers	Stomach Mucosa	stomach
28	chr18:9116600-9119800	Enhancers	Brain Cingulate Gyrus	brain
29	chr18:9116600-9120400	Enhancers	Brain Substantia Nigra	brain
30	chr18:9116800-9119200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr18:9116800-9119800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr18:9116800-9135200	Strong transcription	Fetal Thymus	thymus
33	chr18:9117200-9119200	Enhancers	Fetal Heart	heart
34	chr18:9117200-9119600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:9117200-9134800	Weak transcription	Brain Germinal Matrix	brain
36	chr18:9117400-9119200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr18:9117400-9119200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr18:9117400-9123400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr18:9117400-9125800	Weak transcription	Right Atrium	heart
40	chr18:9117400-9132000	Strong transcription	Fetal Intestine Large	intestine
41	chr18:9117400-9135200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr18:9117400-9135600	Weak transcription	Esophagus	oesophagus
43	chr18:9117400-9135800	Weak transcription	Gastric	stomach
44	chr18:9117600-9119200	Enhancers	Primary B cells from peripheral blood	blood
45	chr18:9117600-9119200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr18:9117600-9119400	Enhancers	Colon Smooth Muscle	Colon
47	chr18:9117600-9119800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr18:9117600-9123400	Weak transcription	Left Ventricle	heart
49	chr18:9117600-9123400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr18:9117600-9127400	Weak transcription	Spleen	Spleen

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