Variant report

Variant	rs10438889
Chromosome Location	chr18:9287829-9287830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9277321..9279568-chr18:9287387..9289773,2	MCF-7	breast:
2	chr18:9281031..9284071-chr18:9285827..9289702,4	K562	blood:
3	chr18:9279984..9282531-chr18:9286005..9288429,2	K562	blood:

Variant related genes	Relation type
ENSG00000239087	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10163536	0.84[EUR][1000 genomes]
rs10164138	0.84[EUR][1000 genomes]
rs1107146	0.84[EUR][1000 genomes]
rs1107147	0.84[EUR][1000 genomes]
rs17414871	0.84[EUR][1000 genomes]
rs28623301	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2864527	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28687517	0.81[EUR][1000 genomes]
rs2902783	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs57292829	0.84[EUR][1000 genomes]
rs58487677	0.84[EUR][1000 genomes]
rs61257061	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7230937	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7244225	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72939247	0.97[EUR][1000 genomes]
rs72943134	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72943139	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72943143	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72943148	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72943150	0.84[EUR][1000 genomes]
rs72943151	0.84[EUR][1000 genomes]
rs72943156	0.84[EUR][1000 genomes]
rs72943157	0.84[EUR][1000 genomes]
rs72943163	0.84[EUR][1000 genomes]
rs72943167	0.84[EUR][1000 genomes]
rs72943168	0.84[EUR][1000 genomes]
rs72943173	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1055696	chr18:9191679-9309805	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv458023	chr18:9240413-9357786	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv576447	chr18:9240413-9357786	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9216000-9289600	Weak transcription	HMEC	breast
2	chr18:9234800-9290000	Weak transcription	NHLF	lung
3	chr18:9265600-9288400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:9265600-9289600	Weak transcription	Esophagus	oesophagus
5	chr18:9265600-9291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:9265600-9292400	Weak transcription	Aorta	Aorta
7	chr18:9265600-9298200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:9265800-9290000	Weak transcription	HSMMtube	muscle
9	chr18:9276600-9288400	Weak transcription	Ovary	ovary
10	chr18:9278600-9290200	Weak transcription	HepG2	liver
11	chr18:9279000-9288200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr18:9279400-9290000	Weak transcription	Fetal Lung	lung
13	chr18:9280600-9292400	Weak transcription	Pancreas	Pancrea
14	chr18:9280600-9293000	Weak transcription	Fetal Muscle Leg	muscle
15	chr18:9280800-9290000	Weak transcription	Fetal Stomach	stomach
16	chr18:9281200-9289600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr18:9281200-9290000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr18:9281200-9292400	Weak transcription	Lung	lung
19	chr18:9281200-9292600	Weak transcription	Thymus	Thymus
20	chr18:9281400-9290400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr18:9281600-9290200	Weak transcription	Placenta	Placenta
22	chr18:9282000-9292800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr18:9283000-9292200	Weak transcription	HSMM	muscle
24	chr18:9283200-9290000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr18:9283400-9289800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr18:9284000-9288400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr18:9284200-9292600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr18:9284400-9289800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr18:9284400-9290200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr18:9284400-9292600	Weak transcription	Primary B cells from cord blood	blood
31	chr18:9284600-9290200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr18:9284800-9290800	Weak transcription	Liver	Liver
33	chr18:9284800-9290800	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links