Variant report

Variant	rs2705551
Chromosome Location	chr3:112310253-112310254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112305089..112306971-chr3:112309621..112312159,2	MCF-7	breast:
2	chr3:112308556..112310360-chr3:112358622..112360882,2	MCF-7	breast:
3	chr3:112309559..112314656-chr3:112358465..112361451,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10934177	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385527	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386896	1.00[ASN][1000 genomes]
rs1388442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472106	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472107	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488260	1.00[ASN][1000 genomes]
rs1488262	1.00[ASN][1000 genomes]
rs1491629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532198	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552707	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814053	1.00[ASN][1000 genomes]
rs1817694	1.00[ASN][1000 genomes]
rs1844864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877362	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877364	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906519	1.00[ASN][1000 genomes]
rs2029317	1.00[ASN][1000 genomes]
rs2399431	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638033	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638034	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638036	1.00[ASN][1000 genomes]
rs2638041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638043	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668216	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2705510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705514	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705524	1.00[ASN][1000 genomes]
rs2705554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969894	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109033	0.86[ASN][1000 genomes]
rs62264580	0.83[ASN][1000 genomes]
rs6793232	1.00[ASN][1000 genomes]
rs7618978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901829	1.00[ASN][1000 genomes]
rs971832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
3	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
4	chr3:112281800-112325400	Weak transcription	Gastric	stomach
5	chr3:112282000-112312200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
8	chr3:112282400-112312400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:112282400-112316800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:112283000-112316400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:112290400-112317400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:112290600-112315600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:112291600-112320600	Weak transcription	NHLF	lung
17	chr3:112293200-112315600	Weak transcription	NH-A	brain
18	chr3:112293200-112318000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:112295400-112311200	Weak transcription	Fetal Intestine Small	intestine
20	chr3:112298600-112325200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:112299200-112311000	Weak transcription	HUVEC	blood vessel
23	chr3:112299200-112311000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr3:112299200-112315000	Weak transcription	NHEK	skin
25	chr3:112300200-112315800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:112300200-112317400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:112300200-112331000	Weak transcription	Lung	lung
28	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
29	chr3:112301200-112311200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:112301600-112315600	Weak transcription	Stomach Mucosa	stomach
31	chr3:112301600-112316600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:112301800-112311600	Weak transcription	A549	lung
33	chr3:112302000-112313800	Weak transcription	Dnd41	blood
34	chr3:112302000-112317400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:112302600-112322800	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:112302800-112324200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:112303400-112317000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:112303600-112322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:112303800-112311000	Weak transcription	GM12878-XiMat	blood
40	chr3:112303800-112312200	Weak transcription	Brain Angular Gyrus	brain
41	chr3:112303800-112324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:112304000-112311400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:112304000-112320400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:112304200-112311400	Weak transcription	Psoas Muscle	Psoas
45	chr3:112304200-112317600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:112304400-112312000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:112304400-112312000	Weak transcription	Ovary	ovary
48	chr3:112304600-112311200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:112305000-112311400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:112305000-112315000	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links