Variant report

Variant	rs2518106
Chromosome Location	chr9:108395932-108395933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108395259..108397968-chr9:108400674..108403020,2	MCF-7	breast:
2	chr9:108395582..108398707-chr9:108398809..108401541,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10115299	0.82[EUR][1000 genomes]
rs10761100	0.82[EUR][1000 genomes]
rs10816278	0.86[EUR][1000 genomes]
rs10820809	0.82[EUR][1000 genomes]
rs10820810	0.88[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs10820813	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1360089	0.89[EUR][1000 genomes]
rs1815383	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs1960023	0.80[JPT][hapmap]
rs1987634	0.88[EUR][1000 genomes]
rs2225246	0.90[EUR][1000 genomes]
rs2427769	0.87[EUR][1000 genomes]
rs2518112	0.91[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2518114	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs2518116	0.80[JPT][hapmap]
rs2518120	0.91[CEU][hapmap];0.80[JPT][hapmap];0.93[EUR][1000 genomes]
rs2518123	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2518128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2518131	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2768280	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2768283	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs2768290	0.96[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2768291	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs2768294	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2771038	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2771041	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2771042	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2812303	0.91[CEU][hapmap]
rs2812308	0.87[EUR][1000 genomes]
rs2812310	0.82[CHB][hapmap];0.86[GIH][hapmap]
rs4742947	0.90[EUR][1000 genomes]
rs4742948	0.92[EUR][1000 genomes]
rs6477449	0.94[EUR][1000 genomes]
rs7020083	0.90[EUR][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	nsv519023	chr9:108371549-108454745	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108321600-108397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:108333200-108400400	Weak transcription	HMEC	breast
3	chr9:108335400-108403400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:108338400-108403400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:108345600-108400000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr9:108347000-108399600	Weak transcription	Psoas Muscle	Psoas
7	chr9:108349400-108402200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:108350800-108403800	Weak transcription	Fetal Heart	heart
9	chr9:108354400-108397200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:108354400-108397400	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:108354400-108400000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr9:108354400-108403600	Weak transcription	Brain Substantia Nigra	brain
13	chr9:108354400-108412400	Weak transcription	Right Ventricle	heart
14	chr9:108354600-108397000	Weak transcription	Fetal Muscle Leg	muscle
15	chr9:108354600-108397200	Weak transcription	Aorta	Aorta
16	chr9:108354600-108401600	Weak transcription	GM12878-XiMat	blood
17	chr9:108354600-108412200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:108354800-108396400	Weak transcription	Fetal Stomach	stomach
19	chr9:108355200-108404200	Weak transcription	Brain Germinal Matrix	brain
20	chr9:108355200-108409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:108355800-108396800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:108355800-108397200	Weak transcription	Ovary	ovary
23	chr9:108356000-108403800	Weak transcription	Fetal Thymus	thymus
24	chr9:108358200-108405000	Weak transcription	HUVEC	blood vessel
25	chr9:108359800-108397000	Weak transcription	Liver	Liver
26	chr9:108360600-108397000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr9:108361000-108397200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:108366800-108396800	Weak transcription	NHDF-Ad	bronchial
29	chr9:108366800-108397000	Weak transcription	Dnd41	blood
30	chr9:108366800-108397200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:108366800-108401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:108366800-108403400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr9:108366800-108405400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr9:108366800-108418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr9:108366800-108418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:108367200-108396200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:108367200-108396800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:108367200-108399600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:108367200-108399600	Weak transcription	Fetal Intestine Large	intestine
40	chr9:108367200-108402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:108367200-108403400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:108367400-108396800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr9:108367400-108407800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:108372200-108402200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:108373000-108397000	Weak transcription	Lung	lung
46	chr9:108373200-108398800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:108373200-108404600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr9:108373400-108398600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:108373600-108397400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:108374200-108397400	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links