Variant report

Variant	rs2061800
Chromosome Location	chr9:97797501-97797502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97796997..97799888-chr9:97851480..97854262,2	MCF-7	breast:
2	chr9:97796632..97799193-chr9:97809608..97812323,2	MCF-7	breast:
3	chr9:97795205..97797752-chr9:97832008..97833533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1004373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10117370	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119512	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10121760	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123819	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1020963	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10512253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761364	0.88[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10761366	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10761368	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10761369	0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs10993427	0.89[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10993464	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993467	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113102	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1412488	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1564234	0.89[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1571894	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1571895	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404295	0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs2404302	0.89[CHB][hapmap]
rs2404305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802454	0.89[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3802456	0.89[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3858089	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4537362	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743980	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743981	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743982	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744422	0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744423	0.89[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744426	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744428	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4744430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744431	0.88[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744435	0.84[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4744436	0.83[JPT][hapmap];0.92[AMR][1000 genomes]
rs6479588	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6479591	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479592	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020709	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7021351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7022452	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7043705	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7048786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7048941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7851173	0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7854831	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7857679	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7862156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7863291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7865144	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7871218	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7873479	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7873567	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs962229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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 miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2061800	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97789000-97806200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:97791600-97799600	Weak transcription	Hela-S3	cervix
4	chr9:97791600-97800000	Weak transcription	Placenta	Placenta
5	chr9:97793000-97800000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:97793200-97802200	Weak transcription	Fetal Kidney	kidney
7	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
8	chr9:97793600-97798200	Weak transcription	NHDF-Ad	bronchial
9	chr9:97793800-97800000	Weak transcription	Adipose Nuclei	Adipose
10	chr9:97794000-97799800	Weak transcription	Fetal Lung	lung
11	chr9:97794200-97805800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:97794200-97807000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:97794400-97806000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:97794600-97800000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:97794600-97800000	Weak transcription	Colonic Mucosa	Colon
16	chr9:97794600-97805000	Weak transcription	Fetal Thymus	thymus
17	chr9:97794800-97798200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:97794800-97798200	Weak transcription	NHLF	lung
19	chr9:97794800-97799800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:97795000-97798200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:97795000-97799200	Weak transcription	HMEC	breast
22	chr9:97795000-97802200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:97795000-97810400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:97795200-97804000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:97795400-97798000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:97795400-97799000	Enhancers	Rectal Smooth Muscle	rectum
27	chr9:97795400-97800000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr9:97795400-97800000	Weak transcription	Gastric	stomach
29	chr9:97795400-97803000	Enhancers	Colon Smooth Muscle	Colon
30	chr9:97795400-97806200	Genic enhancers	A549	lung
31	chr9:97795600-97797600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr9:97795600-97797600	Strong transcription	NHEK	skin
33	chr9:97795600-97798200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:97795600-97798200	Strong transcription	Liver	Liver
35	chr9:97795600-97798200	Weak transcription	Fetal Intestine Large	intestine
36	chr9:97795600-97798200	Weak transcription	Fetal Stomach	stomach
37	chr9:97795600-97798400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr9:97795600-97799000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:97795600-97799000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:97795600-97799200	Weak transcription	NH-A	brain
41	chr9:97795600-97799800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr9:97795600-97802200	Weak transcription	Spleen	Spleen
43	chr9:97795600-97806000	Weak transcription	Lung	lung
44	chr9:97795600-97808600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr9:97795800-97797600	Enhancers	Fetal Heart	heart
46	chr9:97795800-97798200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr9:97795800-97798200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:97795800-97798200	Strong transcription	Osteobl	bone
49	chr9:97795800-97798400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:97795800-97798400	Weak transcription	Brain Hippocampus Middle	brain

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