Variant report

Variant	rs10869440
Chromosome Location	chr9:71483661-71483662
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71481298..71483718-chr9:71491074..71493993,2	MCF-7	breast:
2	chr9:71477461..71479791-chr9:71480861..71483693,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10511961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10781249	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10869327	0.80[EUR][1000 genomes]
rs10869422	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10869434	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10869441	0.95[CEU][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869442	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10869451	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11143793	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs11144011	0.89[ASN][1000 genomes]
rs11144057	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11144066	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11144133	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11144167	0.95[ASN][1000 genomes]
rs17392931	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2152647	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55845142	0.88[ASN][1000 genomes]
rs62566867	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6560397	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs68060556	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7040065	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs72720041	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867287	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
15	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71438000-71491200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:71448200-71485600	Weak transcription	Stomach Mucosa	stomach
3	chr9:71459000-71519200	Weak transcription	Colonic Mucosa	Colon
4	chr9:71460400-71495600	Weak transcription	Aorta	Aorta
5	chr9:71460800-71517000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr9:71463400-71492800	Weak transcription	GM12878-XiMat	blood
7	chr9:71463600-71501800	Weak transcription	Small Intestine	intestine
8	chr9:71467800-71495800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:71468200-71486600	Weak transcription	Left Ventricle	heart
10	chr9:71474600-71492400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:71474800-71501800	Weak transcription	Right Ventricle	heart
12	chr9:71477000-71485600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:71477800-71483800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr9:71478000-71486000	Strong transcription	Primary B cells from cord blood	blood
15	chr9:71479200-71501600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:71480800-71483800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:71480800-71486200	Weak transcription	Gastric	stomach
18	chr9:71480800-71495600	Weak transcription	Lung	lung
19	chr9:71480800-71495600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:71480800-71501200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:71481000-71485000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr9:71481200-71485600	Weak transcription	HepG2	liver
23	chr9:71481200-71504000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr9:71481800-71483800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:71482000-71492600	Weak transcription	Fetal Intestine Large	intestine
26	chr9:71482400-71495200	Weak transcription	Fetal Intestine Small	intestine
27	chr9:71482600-71486800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr9:71482800-71485200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr9:71483400-71484200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:71483400-71484800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:71483400-71486800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr9:71483400-71486800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr9:71483400-71487000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr9:71483400-71487400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr9:71483600-71484200	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr9:71483600-71484600	Enhancers	Fetal Heart	heart
37	chr9:71483600-71484600	Enhancers	Rectal Smooth Muscle	rectum
38	chr9:71483600-71486800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr9:71483600-71486800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr9:71483600-71487000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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