Variant report

Variant	rs17005485
Chromosome Location	chr4:120648487-120648488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120648083..120649725-chr4:120663986..120665688,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10005075	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10005177	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10007283	0.80[EUR][1000 genomes]
rs10011345	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10011928	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10014793	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10018153	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10018308	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10019790	0.95[ASN][1000 genomes]
rs10023652	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10023655	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12331776	0.82[EUR][1000 genomes]
rs12502919	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12510467	0.82[EUR][1000 genomes]
rs13112498	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13119146	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13122357	0.82[EUR][1000 genomes]
rs13141413	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13328038	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17005677	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2389900	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389902	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389904	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714972	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28535991	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28642385	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28701469	0.81[AFR][1000 genomes]
rs28706824	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28723049	0.81[EUR][1000 genomes]
rs28847617	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34209241	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4001169	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833625	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4834804	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4834805	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4834806	0.88[ASN][1000 genomes]
rs4834808	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs749525	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs749526	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs752650	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7669436	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694773	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7699252	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs874425	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9998665	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9999212	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS 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	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1010638	chr4:120586178-120671835	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1009771	chr4:120590902-120665812	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv3446791	chr4:120621398-120649319	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17005485	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs17005485	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs17005485	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120642800-120650200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:120644200-120650000	Weak transcription	Liver	Liver
3	chr4:120644200-120650000	Weak transcription	Psoas Muscle	Psoas
4	chr4:120646200-120648800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:120646400-120650000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:120646400-120651400	Weak transcription	Pancreas	Pancrea
7	chr4:120646600-120648800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:120646600-120649400	Enhancers	Osteobl	bone
9	chr4:120646800-120648800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr4:120646800-120648800	Enhancers	NHDF-Ad	bronchial
11	chr4:120646800-120649000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:120647200-120650200	Weak transcription	Fetal Lung	lung
13	chr4:120647400-120650000	Weak transcription	Aorta	Aorta
14	chr4:120647400-120650200	Weak transcription	Fetal Stomach	stomach
15	chr4:120647400-120650400	Weak transcription	Stomach Mucosa	stomach
16	chr4:120647600-120648600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:120647600-120650000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:120647600-120651000	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:120647600-120651400	Weak transcription	Right Atrium	heart
20	chr4:120647600-120651600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:120647600-120651600	Weak transcription	Colonic Mucosa	Colon
22	chr4:120647600-120651800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:120647800-120648600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:120647800-120650200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:120647800-120650200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:120647800-120651000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:120647800-120651400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:120647800-120652200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:120648000-120651000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:120648200-120649600	Weak transcription	NHLF	lung
31	chr4:120648200-120650200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:120648400-120650000	Weak transcription	HSMM	muscle
33	chr4:120648400-120650000	Weak transcription	NH-A	brain
34	chr4:120648400-120650200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links