Variant report

Variant	rs12346261
Chromosome Location	chr9:97785778-97785779
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
2	chr9:97785037..97786966-chr9:97789243..97791413,3	MCF-7	breast:
3	chr9:97783764..97786051-chr9:97788470..97790440,2	K562	blood:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1020963	0.90[JPT][hapmap]
rs10761368	1.00[JPT][hapmap]
rs10821433	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10993381	0.82[CEU][hapmap]
rs10993390	1.00[CEU][hapmap]
rs10993391	1.00[CEU][hapmap]
rs10993456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993457	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10993460	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12337251	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12339639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340107	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs12344052	0.82[CEU][hapmap]
rs12344584	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349263	1.00[CEU][hapmap]
rs1412488	0.90[JPT][hapmap]
rs4744422	0.91[JPT][hapmap]
rs4744431	0.90[JPT][hapmap]
rs6479588	0.91[JPT][hapmap]
rs7023719	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs7046845	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72621414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97768000-97786200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:97769000-97787600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:97769600-97790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
5	chr9:97773200-97793200	Weak transcription	Brain Germinal Matrix	brain
6	chr9:97777400-97794200	Weak transcription	Thymus	Thymus
7	chr9:97778800-97786200	Genic enhancers	Osteobl	bone
8	chr9:97779400-97789200	Genic enhancers	Liver	Liver
9	chr9:97780200-97788000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:97780200-97788200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:97780600-97786600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:97780600-97790800	Weak transcription	Fetal Brain Female	brain
13	chr9:97780800-97786000	Genic enhancers	Left Ventricle	heart
14	chr9:97781000-97786400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:97781200-97786400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:97781200-97787400	Genic enhancers	NHLF	lung
17	chr9:97781200-97793600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:97781400-97786200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:97781400-97793200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:97781400-97793600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:97781600-97786200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:97781600-97787000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:97781600-97787200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr9:97782000-97792800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:97782400-97786000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr9:97782600-97793600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr9:97782800-97786200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:97782800-97787600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:97783200-97789400	Enhancers	Brain Substantia Nigra	brain
30	chr9:97783400-97789000	Transcr. at gene 5' and 3'	A549	lung
31	chr9:97783600-97794000	Weak transcription	GM12878-XiMat	blood
32	chr9:97783800-97789000	Genic enhancers	HSMMtube	muscle
33	chr9:97783800-97789600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:97784000-97786400	Enhancers	Rectal Smooth Muscle	rectum
35	chr9:97784200-97786600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:97784200-97786600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr9:97784200-97786600	Weak transcription	Gastric	stomach
38	chr9:97784200-97787600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:97784200-97789200	Enhancers	Brain Hippocampus Middle	brain
40	chr9:97784400-97787400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:97784400-97788800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr9:97784400-97789000	Genic enhancers	NHEK	skin
43	chr9:97784600-97789000	Enhancers	Brain Cingulate Gyrus	brain
44	chr9:97785000-97785800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:97785000-97785800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
46	chr9:97785000-97786000	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr9:97785000-97786600	Enhancers	HUVEC	blood vessel
48	chr9:97785000-97787000	Enhancers	Small Intestine	intestine
49	chr9:97785000-97787800	Genic enhancers	Fetal Stomach	stomach
50	chr9:97785000-97788400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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