Variant report

Variant	rs2404305
Chromosome Location	chr9:97801706-97801707
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97798563..97802420-chr9:97810899..97813846,4	MCF-7	breast:
2	chr9:97801094..97803225-chr9:97809368..97812078,2	K562	blood:
3	chr9:97800986..97803575-chr9:97807961..97810868,3	K562	blood:
4	chr9:97799418..97802536-chr9:97804091..97807017,3	MCF-7	breast:
5	chr9:97800135..97801967-chr9:97807867..97810456,2	MCF-7	breast:
6	chr9:97794089..97795756-chr9:97801437..97804399,2	K562	blood:
7	chr9:97799572..97803967-chr9:97808050..97811094,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1004373	1.00[CEU][hapmap];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	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10512253	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761364	0.91[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][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	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10761369	0.83[CEU][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs10993427	0.88[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10993456	0.82[TSI][hapmap]
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]
rs12339639	0.82[TSI][hapmap]
rs1412488	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1564234	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1571894	1.00[CEU][hapmap];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	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2061800	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]
rs2404295	0.87[CHD][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs2404302	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs2404456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802454	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3802456	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.89[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[CEU][hapmap];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[CEU][hapmap];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	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744422	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744423	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744424	1.00[CEU][hapmap];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[CEU][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][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	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744431	0.91[CEU][hapmap];0.87[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744432	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744433	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744435	0.82[CEU][hapmap];0.84[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4744436	0.91[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes]
rs6479588	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6479591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020709	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7021351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7022452	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7048941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7851173	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][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	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2404305	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL
rs2404305	OGN	cis	parietal	SCAN
rs2404305	FOXE1	cis	parietal	SCAN

Chromatin state (count:87 , 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	chr9:97793200-97802200	Weak transcription	Fetal Kidney	kidney
4	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
5	chr9:97794200-97805800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:97794200-97807000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:97794400-97806000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:97794600-97805000	Weak transcription	Fetal Thymus	thymus
9	chr9:97795000-97802200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:97795000-97810400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:97795200-97804000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:97795400-97803000	Enhancers	Colon Smooth Muscle	Colon
13	chr9:97795400-97806200	Genic enhancers	A549	lung
14	chr9:97795600-97802200	Weak transcription	Spleen	Spleen
15	chr9:97795600-97806000	Weak transcription	Lung	lung
16	chr9:97795600-97808600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:97795800-97802200	Weak transcription	Small Intestine	intestine
18	chr9:97796600-97802200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:97797000-97807800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:97798200-97804400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:97798200-97808600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr9:97799000-97801800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr9:97799000-97803200	Genic enhancers	Left Ventricle	heart
24	chr9:97799400-97802200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:97799400-97802200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:97799400-97807600	Weak transcription	Thymus	Thymus
27	chr9:97799400-97810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:97799600-97802800	Strong transcription	Hela-S3	cervix
29	chr9:97799800-97801800	Enhancers	HMEC	breast
30	chr9:97799800-97805400	Enhancers	Brain Cingulate Gyrus	brain
31	chr9:97799800-97806800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:97800000-97808600	Genic enhancers	Liver	Liver
33	chr9:97800200-97802600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr9:97800200-97806200	Strong transcription	Osteobl	bone
35	chr9:97800400-97802200	Weak transcription	Fetal Intestine Large	intestine
36	chr9:97800400-97802200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:97800400-97802200	Weak transcription	NHLF	lung
38	chr9:97800400-97802400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:97800400-97802400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:97800400-97802400	Weak transcription	Right Ventricle	heart
41	chr9:97800400-97802600	Weak transcription	Ovary	ovary
42	chr9:97800400-97802800	Strong transcription	Fetal Stomach	stomach
43	chr9:97800400-97806000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:97800400-97806000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:97800600-97801800	Enhancers	Placenta	Placenta
46	chr9:97800600-97801800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:97800600-97804200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:97800600-97805600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr9:97800600-97806000	Weak transcription	Adipose Nuclei	Adipose
50	chr9:97800800-97802200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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