Variant report

Variant	rs12554172
Chromosome Location	chr9:100797597-100797598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100797529..100799265-chr9:100810758..100812808,2	K562	blood:
2	chr9:100684268..100684829-chr9:100796846..100797760,2	K562	blood:
3	chr9:100684661..100686943-chr9:100794140..100799259,5	K562	blood:
4	chr9:100685383..100686650-chr9:100796663..100797820,11	K562	blood:
5	chr9:100744061..100747104-chr9:100795931..100798859,4	MCF-7	breast:
6	chr9:100685498..100686359-chr9:100796718..100798043,9	MCF-7	breast:
7	chr9:100793900..100798932-chr9:100816820..100821233,8	MCF-7	breast:
8	chr9:100796342..100798790-chr9:101837762..101839571,2	K562	blood:
9	chr9:100796501..100799835-chr9:100807798..100809968,3	K562	blood:
10	chr9:100797145..100798657-chr9:100798784..100800862,2	K562	blood:
11	chr9:100684056..100686567-chr9:100797424..100799144,2	MCF-7	breast:
12	chr9:100789228..100794108-chr9:100794751..100799924,8	K562	blood:
13	chr9:100776438..100779728-chr9:100795602..100798720,4	K562	blood:
14	chr9:100705623..100707205-chr9:100796922..100798794,2	K562	blood:
15	chr9:100779685..100780554-chr9:100797234..100797778,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000136929	Chromatin interaction
ENSG00000095380	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1059273	0.80[CEU][hapmap]
rs12001675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16912622	0.80[CEU][hapmap]
rs3739672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742716	0.80[CEU][hapmap]
rs4743150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743151	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743157	0.80[CEU][hapmap]
rs4743158	0.82[CEU][hapmap]
rs6478522	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6478539	0.80[CEU][hapmap]
rs6478556	0.80[CEU][hapmap]
rs7019033	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7020081	0.82[CEU][hapmap]
rs7041878	0.82[ASN][1000 genomes]
rs7850685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7852752	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7855432	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7869762	0.80[CEU][hapmap]
rs874610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs957955	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[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	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv3493282	chr9:100784615-100805700	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3493283	chr9:100784615-100805700	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100784000-100803800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:100785000-100801400	Weak transcription	Fetal Intestine Small	intestine
3	chr9:100795600-100800200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:100796800-100797600	Enhancers	HSMM	muscle
5	chr9:100796800-100797600	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr9:100796800-100797800	Enhancers	Esophagus	oesophagus
7	chr9:100796800-100797800	Enhancers	Right Ventricle	heart
8	chr9:100796800-100798000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:100796800-100798000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:100796800-100798000	Enhancers	Placenta	Placenta
11	chr9:100796800-100798200	Enhancers	Fetal Muscle Leg	muscle
12	chr9:100796800-100798200	Flanking Active TSS	GM12878-XiMat	blood
13	chr9:100796800-100798400	Enhancers	Fetal Muscle Trunk	muscle
14	chr9:100796800-100798800	Enhancers	Primary B cells from peripheral blood	blood
15	chr9:100796800-100799600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr9:100797000-100797600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr9:100797000-100797600	Enhancers	Osteobl	bone
18	chr9:100797000-100798000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:100797000-100798000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:100797000-100798000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:100797000-100798000	Enhancers	Psoas Muscle	Psoas
22	chr9:100797000-100798000	Enhancers	Spleen	Spleen
23	chr9:100797000-100798000	Enhancers	NHDF-Ad	bronchial
24	chr9:100797000-100798000	Enhancers	NHEK	skin
25	chr9:100797000-100798200	Enhancers	Primary B cells from cord blood	blood
26	chr9:100797000-100798200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:100797000-100798200	Enhancers	HMEC	breast
28	chr9:100797000-100798200	Enhancers	HUVEC	blood vessel
29	chr9:100797000-100798200	Enhancers	NH-A	brain
30	chr9:100797200-100797600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr9:100797200-100797600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:100797200-100797600	Enhancers	Colon Smooth Muscle	Colon
33	chr9:100797200-100797600	Enhancers	Stomach Smooth Muscle	stomach
34	chr9:100797200-100797600	Bivalent Enhancer	HepG2	liver
35	chr9:100797200-100797800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr9:100797200-100797800	Enhancers	A549	lung
37	chr9:100797200-100798000	Enhancers	Hela-S3	cervix
38	chr9:100797200-100799000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:100797200-100799000	Weak transcription	Right Atrium	heart
40	chr9:100797200-100799200	Weak transcription	Left Ventricle	heart
41	chr9:100797200-100799200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr9:100797200-100799600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:100797200-100799600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr9:100797200-100799800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr9:100797200-100799800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr9:100797200-100800200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:100797200-100800200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:100797400-100797800	Enhancers	K562	blood
49	chr9:100797400-100798000	Enhancers	HSMMtube	muscle
50	chr9:100797400-100798000	Enhancers	NHLF	lung

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