Variant report

Variant	rs6544187
Chromosome Location	chr2:39232275-39232276
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39231626..39234527-chr2:39249875..39251699,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10172714	0.93[AMR][1000 genomes]
rs10183915	0.83[ASN][1000 genomes]
rs10186762	0.93[AMR][1000 genomes]
rs10192250	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10201980	0.89[AMR][1000 genomes]
rs10439459	0.81[ASN][1000 genomes]
rs10779924	0.86[AMR][1000 genomes]
rs11124659	0.82[ASN][1000 genomes]
rs13023273	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1454221	0.93[AMR][1000 genomes]
rs1454222	0.93[AMR][1000 genomes]
rs1454223	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1454225	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1869513	0.82[AMR][1000 genomes]
rs1869514	0.83[AMR][1000 genomes]
rs1947432	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2123876	0.85[ASN][1000 genomes]
rs2168044	0.86[AMR][1000 genomes]
rs2278912	0.93[AMR][1000 genomes]
rs2278913	0.89[AMR][1000 genomes]
rs2278914	0.93[AMR][1000 genomes]
rs2290445	0.93[AMR][1000 genomes]
rs2305516	0.89[AMR][1000 genomes]
rs2603145	0.84[AMR][1000 genomes]
rs371745	0.89[AMR][1000 genomes]
rs3765058	0.89[AMR][1000 genomes]
rs4142729	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs422854	0.86[AMR][1000 genomes]
rs4643520	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4670270	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4670901	0.89[AMR][1000 genomes]
rs4670903	0.86[AMR][1000 genomes]
rs6544183	0.86[AMR][1000 genomes]
rs6544184	0.89[AMR][1000 genomes]
rs6544191	0.83[ASN][1000 genomes]
rs6704656	0.89[AMR][1000 genomes]
rs6713281	0.81[ASN][1000 genomes]
rs6716101	0.89[AMR][1000 genomes]
rs6752850	0.93[AMR][1000 genomes]
rs6755527	0.86[AMR][1000 genomes]
rs7568552	0.86[ASN][1000 genomes]
rs7571052	0.86[AMR][1000 genomes]
rs7573310	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7577088	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7594644	0.86[AMR][1000 genomes]
rs9679498	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6544187	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
2	chr2:39206000-39235800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:39210400-39233200	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
5	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:39211400-39237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
10	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
11	chr2:39213400-39234400	Weak transcription	Gastric	stomach
12	chr2:39213400-39234400	Weak transcription	NHEK	skin
13	chr2:39213400-39242200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:39213400-39242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
17	chr2:39213800-39235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:39213800-39235000	Weak transcription	Small Intestine	intestine
19	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
20	chr2:39214200-39235400	Weak transcription	Hela-S3	cervix
21	chr2:39217400-39241800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:39217600-39234200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:39217600-39242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:39217600-39244200	Strong transcription	Primary B cells from cord blood	blood
25	chr2:39218800-39241200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:39219200-39244000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:39219400-39242600	Weak transcription	Brain Substantia Nigra	brain
29	chr2:39220400-39233000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:39220600-39237000	Strong transcription	Fetal Thymus	thymus
31	chr2:39221000-39241200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:39223600-39235000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:39224400-39233800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:39225000-39233200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:39225200-39233200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr2:39225400-39241800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:39225600-39235600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:39225600-39241600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr2:39225600-39241600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:39225600-39241600	Strong transcription	Placenta	Placenta
41	chr2:39225800-39233600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:39225800-39238000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:39225800-39241200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:39226000-39232800	Strong transcription	Osteobl	bone
45	chr2:39226200-39241600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:39226400-39235000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:39226600-39235000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:39227000-39235800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:39227200-39235000	Weak transcription	Esophagus	oesophagus
50	chr2:39227400-39234400	Weak transcription	Aorta	Aorta

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