Variant report

Variant	rs6755527
Chromosome Location	chr2:39187190-39187191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:39186935-39188239	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBP	chr2:39187051-39187682	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:39187115-39187751	HUVEC	blood vessel:	n/a	n/a
4	E2F6	chr2:39186598-39188433	H1-hESC	embryonic stem cell:	n/a	chr2:39186906-39186916 chr2:39187950-39187960 chr2:39187901-39187911
5	E2F6	chr2:39186760-39188342	H1-hESC	embryonic stem cell:	n/a	chr2:39186906-39186916 chr2:39187950-39187960 chr2:39187901-39187911
6	POLR2A	chr2:39187077-39187717	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr2:39186582-39188333	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr2:39187080-39187230	HUVEC	blood vessel:	n/a	n/a
9	MAX	chr2:39186987-39188223	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr2:39186952-39188079	IMR90	lung:	n/a	n/a
11	MAX	chr2:39187013-39187846	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39183680..39185526-chr2:39186357..39188173,2	MCF-7	breast:

Variant related genes	Relation type
ARHGEF33	TF binding region
ENSG00000214694	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10172714	0.92[AMR][1000 genomes]
rs10186762	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10192250	0.89[AMR][1000 genomes]
rs10201980	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10779924	0.86[AMR][1000 genomes]
rs13023273	0.92[AMR][1000 genomes]
rs1454221	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1454222	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1454223	0.92[AMR][1000 genomes]
rs1454225	0.92[AMR][1000 genomes]
rs1869513	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1869514	0.83[AMR][1000 genomes]
rs1947432	0.92[AMR][1000 genomes]
rs2168044	0.86[AMR][1000 genomes]
rs2278912	0.92[AMR][1000 genomes]
rs2278913	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2278914	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2290445	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2305516	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs371745	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3765058	0.89[AMR][1000 genomes]
rs4142729	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs422854	0.86[AMR][1000 genomes]
rs4643520	0.92[AMR][1000 genomes]
rs4670270	0.92[AMR][1000 genomes]
rs4670901	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4670903	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6544183	0.86[AMR][1000 genomes]
rs6544184	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6544187	0.86[AMR][1000 genomes]
rs6704656	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6716101	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6752850	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7571052	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7573310	0.92[AMR][1000 genomes]
rs7577088	0.89[AMR][1000 genomes]
rs7594644	0.86[AMR][1000 genomes]
rs958412	0.83[AMR][1000 genomes]
rs9679498	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6755527	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39186600-39187200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:39186600-39187200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr2:39186600-39187200	Enhancers	Pancreas	Pancrea
4	chr2:39186600-39187400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:39186600-39187800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr2:39186600-39188200	Enhancers	Fetal Brain Male	brain
7	chr2:39186600-39188400	Active TSS	Rectal Smooth Muscle	rectum
8	chr2:39186800-39187200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr2:39186800-39187200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr2:39186800-39187200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:39186800-39187200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
12	chr2:39186800-39187200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:39186800-39187200	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr2:39186800-39187200	Flanking Active TSS	Ovary	ovary
15	chr2:39186800-39187200	Enhancers	Spleen	Spleen
16	chr2:39186800-39187400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
17	chr2:39186800-39187400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
18	chr2:39186800-39187600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:39186800-39187600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr2:39186800-39188000	Active TSS	Brain Substantia Nigra	brain
21	chr2:39186800-39188000	Active TSS	Colon Smooth Muscle	Colon
22	chr2:39186800-39188000	Enhancers	Fetal Heart	heart
23	chr2:39186800-39188200	Active TSS	Brain Cingulate Gyrus	brain
24	chr2:39186800-39188200	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr2:39186800-39188400	Active TSS	Brain Germinal Matrix	brain
26	chr2:39186800-39188400	Active TSS	Fetal Brain Female	brain
27	chr2:39187000-39187200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:39187000-39187200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr2:39187000-39187200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr2:39187000-39187200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
32	chr2:39187000-39187200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:39187000-39187200	Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
35	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:39187000-39187200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
38	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:39187000-39187200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
42	chr2:39187000-39187200	Enhancers	Esophagus	oesophagus
43	chr2:39187000-39187200	ZNF genes & repeats	Fetal Intestine Large	intestine
44	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
46	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
47	chr2:39187000-39187200	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr2:39187000-39187200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
49	chr2:39187000-39187200	Enhancers	HMEC	breast
50	chr2:39187000-39187400	Flanking Active TSS	Primary hematopoietic stem cells	blood

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