Variant report

Variant	rs10981890
Chromosome Location	chr9:100149826-100149827
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100149345..100149902-chr9:100161061..100161631,4	K562	blood:
2	chr9:100149689..100151422-chr9:100157235..100158759,2	MCF-7	breast:
3	chr9:100149241..100149908-chr9:100249138..100249846,2	MCF-7	breast:
4	chr9:100149125..100151047-chr9:100151218..100153967,3	K562	blood:
5	chr9:100149125..100152015-chr9:100152467..100154475,2	K562	blood:
6	chr9:100148966..100149836-chr9:100377517..100378454,2	K562	blood:
7	chr9:100149625..100153516-chr9:100159731..100163036,3	MCF-7	breast:
8	chr9:100148865..100149895-chr9:100161070..100162054,16	MCF-7	breast:
9	chr9:100148981..100149950-chr9:100161161..100161940,4	MCF-7	breast:
10	chr9:100148987..100149894-chr9:100173635..100174632,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196116	Chromatin interaction
ENSG00000228957	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10122063	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10125198	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1020884	0.90[EUR][1000 genomes]
rs1020885	0.90[EUR][1000 genomes]
rs1037948	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1037950	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1037951	0.90[EUR][1000 genomes]
rs10435867	0.90[ASN][1000 genomes]
rs10435868	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10448274	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10759527	0.81[CEU][hapmap]
rs10759624	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10759657	0.90[EUR][1000 genomes]
rs10817273	0.82[CEU][hapmap]
rs10817286	0.82[CEU][hapmap]
rs10817487	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10981280	0.83[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap]
rs10981288	0.83[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap]
rs10981296	0.89[YRI][hapmap]
rs10981329	0.83[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap]
rs10981919	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10981931	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs11581	0.86[JPT][hapmap]
rs11791310	0.83[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap]
rs13298346	0.83[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap]
rs13299627	0.83[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap]
rs1542506	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs1544203	0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap]
rs1903635	0.81[JPT][hapmap]
rs1947717	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2169456	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2219664	0.87[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap]
rs2242187	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279114	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306097	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2502644	0.88[JPT][hapmap]
rs2615143	0.87[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap]
rs2615145	0.87[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap]
rs2795367	0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap]
rs2818238	0.87[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap]
rs2818243	0.90[JPT][hapmap];0.94[YRI][hapmap]
rs3214072	0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs3747489	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3747493	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747496	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3802471	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4237189	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4313271	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4366181	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4523385	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4554595	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742685	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4742689	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs4742690	0.90[EUR][1000 genomes]
rs4743072	0.87[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap]
rs4743076	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743077	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743084	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743087	0.92[CEU][hapmap]
rs4743088	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs6478095	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6478131	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7020393	0.82[JPT][hapmap]
rs7042707	0.82[JPT][hapmap]
rs713066	0.87[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap]
rs750674	0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs7869536	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9696167	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036105	chr9:100131266-100171816	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10981890	RP11-498P14.5	cis	lung	GTEx
rs10981890	ANKRD18CP	cis	Thyroid	GTEx
rs10981890	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100141200-100150800	Weak transcription	Lung	lung
2	chr9:100144400-100150000	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr9:100148400-100151200	Enhancers	Pancreas	Pancrea
4	chr9:100148800-100150000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:100148800-100150000	Enhancers	Liver	Liver
6	chr9:100148800-100151200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr9:100148800-100151200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:100149000-100150800	Enhancers	GM12878-XiMat	blood
9	chr9:100149200-100150000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr9:100149200-100150000	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr9:100149200-100150000	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr9:100149200-100150600	Enhancers	Fetal Brain Male	brain
13	chr9:100149200-100150800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr9:100149200-100151600	Enhancers	Primary B cells from peripheral blood	blood
15	chr9:100149200-100151800	Enhancers	Spleen	Spleen
16	chr9:100149200-100152000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:100149400-100150000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr9:100149400-100150000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr9:100149400-100150000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr9:100149400-100150000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
21	chr9:100149400-100150000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
22	chr9:100149400-100150000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:100149400-100150000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:100149400-100150000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:100149400-100150000	Bivalent Enhancer	Adipose Nuclei	Adipose
26	chr9:100149400-100150000	Flanking Active TSS	Colonic Mucosa	Colon
27	chr9:100149400-100150000	Active TSS	Fetal Brain Female	brain
28	chr9:100149400-100150000	Bivalent Enhancer	Placenta	Placenta
29	chr9:100149400-100150000	Enhancers	Left Ventricle	heart
30	chr9:100149400-100150000	Enhancers	Ovary	ovary
31	chr9:100149400-100150000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
32	chr9:100149400-100150000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr9:100149400-100150000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr9:100149400-100150200	Active TSS	HepG2	liver
35	chr9:100149400-100150400	Enhancers	Right Ventricle	heart
36	chr9:100149400-100151800	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr9:100149400-100152000	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr9:100149600-100150000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:100149600-100150000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr9:100149600-100150000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr9:100149600-100150000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr9:100149600-100150000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr9:100149600-100150000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:100149600-100150000	Active TSS	Brain Cingulate Gyrus	brain
45	chr9:100149600-100150000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
46	chr9:100149600-100150800	Weak transcription	Primary B cells from cord blood	blood
47	chr9:100149600-100154400	Weak transcription	Gastric	stomach
48	chr9:100149600-100161400	Weak transcription	Right Atrium	heart
49	chr9:100149800-100150000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr9:100149800-100150000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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