Variant report

Variant	rs12340536
Chromosome Location	chr9:14173675-14173676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:14171238..14174758-chr9:14313381..14316374,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147862	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10114590	0.91[AMR][1000 genomes]
rs10114939	0.91[AMR][1000 genomes]
rs10117741	0.84[AMR][1000 genomes]
rs10120754	0.91[AMR][1000 genomes]
rs10122366	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10122412	0.82[AMR][1000 genomes]
rs10123886	0.91[AMR][1000 genomes]
rs10124557	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10125399	0.82[AMR][1000 genomes]
rs10125421	1.00[AMR][1000 genomes]
rs10810101	0.84[AMR][1000 genomes]
rs10810102	0.82[AMR][1000 genomes]
rs10961388	0.82[AMR][1000 genomes]
rs10961397	0.91[AMR][1000 genomes]
rs10961398	0.84[AMR][1000 genomes]
rs11788568	0.91[AMR][1000 genomes]
rs11789923	0.84[AMR][1000 genomes]
rs12335788	0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12335815	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12341599	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12344875	0.95[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12344913	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12344948	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12349598	0.91[AMR][1000 genomes]
rs12351537	0.84[AMR][1000 genomes]
rs12353469	0.82[AMR][1000 genomes]
rs16931417	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28440824	0.81[AMR][1000 genomes]
rs7027294	0.91[AMR][1000 genomes]
rs7033653	0.91[AMR][1000 genomes]
rs7042124	1.00[AMR][1000 genomes]
rs7042142	1.00[AMR][1000 genomes]
rs7047737	0.91[AMR][1000 genomes]
rs73411963	0.91[AMR][1000 genomes]
rs73645005	0.91[AMR][1000 genomes]
rs7846990	0.91[AMR][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	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv892596	chr9:14145487-14208724	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv892597	chr9:14163383-14233159	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14116600-14179200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:14123800-14198600	Weak transcription	Gastric	stomach
3	chr9:14134000-14181000	Weak transcription	Ovary	ovary
4	chr9:14156800-14175600	Weak transcription	Liver	Liver
5	chr9:14159800-14176600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:14159800-14180200	Weak transcription	Fetal Stomach	stomach
7	chr9:14160600-14181400	Weak transcription	HSMM	muscle
8	chr9:14162400-14175400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:14165000-14180200	Weak transcription	Brain Angular Gyrus	brain
10	chr9:14165600-14179200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:14165800-14178800	Weak transcription	Brain Germinal Matrix	brain
12	chr9:14165800-14178800	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:14165800-14179200	Weak transcription	Fetal Brain Male	brain
14	chr9:14165800-14180200	Weak transcription	Brain Anterior Caudate	brain
15	chr9:14165800-14181800	Weak transcription	Psoas Muscle	Psoas
16	chr9:14166200-14183200	Weak transcription	Esophagus	oesophagus
17	chr9:14168800-14179600	Weak transcription	Fetal Brain Female	brain
18	chr9:14170400-14186200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:14170800-14174000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr9:14170800-14178800	Weak transcription	Aorta	Aorta
21	chr9:14170800-14180200	Weak transcription	Right Atrium	heart
22	chr9:14171400-14176600	Weak transcription	Left Ventricle	heart
23	chr9:14171400-14180200	Weak transcription	Fetal Muscle Leg	muscle
24	chr9:14171600-14178800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:14171600-14178800	Weak transcription	Adipose Nuclei	Adipose
26	chr9:14171600-14179000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:14171600-14179600	Weak transcription	NH-A	brain
28	chr9:14171800-14176800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:14171800-14176800	Weak transcription	HMEC	breast
30	chr9:14171800-14180800	Weak transcription	Osteobl	bone
31	chr9:14172000-14179400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:14172200-14176800	Weak transcription	A549	lung
33	chr9:14172200-14181800	Weak transcription	Right Ventricle	heart
34	chr9:14173400-14173800	Weak transcription	Pancreas	Pancrea
35	chr9:14173600-14173800	Enhancers	Fetal Heart	heart
36	chr9:14173600-14174000	Enhancers	Fetal Lung	lung
37	chr9:14173600-14174400	Strong transcription	HUVEC	blood vessel
38	chr9:14173600-14174600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr9:14173600-14174600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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