Variant report

Variant	rs28371821
Chromosome Location	chr9:71557626-71557627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71545273..71547947-chr9:71556049..71558568,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10114785	0.90[AMR][1000 genomes]
rs10117789	0.90[AMR][1000 genomes]
rs10119445	0.80[AMR][1000 genomes]
rs10124098	0.90[AMR][1000 genomes]
rs10869538	0.99[ASN][1000 genomes]
rs11143755	0.80[AMR][1000 genomes]
rs11143976	0.90[AMR][1000 genomes]
rs11144313	0.99[ASN][1000 genomes]
rs12336788	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12336829	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12337137	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12338217	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12345359	0.94[ASN][1000 genomes]
rs12348156	1.00[ASN][1000 genomes]
rs12348451	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349555	1.00[ASN][1000 genomes]
rs12349647	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350004	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12350205	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12351476	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351485	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351519	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352746	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414945	0.90[AMR][1000 genomes]
rs2027023	0.90[AMR][1000 genomes]
rs2039624	0.90[AMR][1000 genomes]
rs28375745	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28444745	0.97[ASN][1000 genomes]
rs28535486	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3750375	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3750376	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3829061	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4237272	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56994943	0.90[AMR][1000 genomes]
rs61547334	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6560418	0.84[ASN][1000 genomes]
rs7018854	0.96[ASN][1000 genomes]
rs7019202	0.83[ASN][1000 genomes]
rs7021259	0.80[AMR][1000 genomes]
rs7024695	0.80[ASN][1000 genomes]
rs7027620	0.87[ASN][1000 genomes]
rs7035068	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7035892	0.91[ASN][1000 genomes]
rs7041194	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7047250	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048275	0.90[AMR][1000 genomes]
rs7847379	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7849727	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7852244	0.90[AMR][1000 genomes]
rs7855274	0.90[AMR][1000 genomes]
rs7859396	0.97[ASN][1000 genomes]
rs7863960	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7870383	0.84[ASN][1000 genomes]
rs953036	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv614549	chr9:71506459-71659280	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking 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	26 gene(s)	inside rSNPs	diseases
19	esv1833433	chr9:71544920-71598165	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	esv2761530	chr9:71548497-71559537	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71510400-71576200	Weak transcription	Stomach Mucosa	stomach
2	chr9:71514200-71557800	Weak transcription	Lung	lung
3	chr9:71519400-71573000	Weak transcription	Gastric	stomach
4	chr9:71535000-71569600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:71542200-71564400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:71545000-71561600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:71545400-71562400	Weak transcription	K562	blood
8	chr9:71546800-71561000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:71548800-71564200	Weak transcription	Placenta	Placenta
10	chr9:71549200-71562000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:71549200-71566200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr9:71549200-71570000	Weak transcription	Fetal Stomach	stomach
13	chr9:71549600-71569600	Weak transcription	Fetal Kidney	kidney
14	chr9:71553400-71558600	Strong transcription	Fetal Intestine Large	intestine
15	chr9:71553400-71567200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:71553600-71558000	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr9:71553800-71558400	Strong transcription	Primary B cells from cord blood	blood
18	chr9:71553800-71565000	Weak transcription	Pancreas	Pancrea
19	chr9:71554400-71565200	Weak transcription	Small Intestine	intestine
20	chr9:71554400-71569600	Weak transcription	Aorta	Aorta
21	chr9:71554800-71558000	Enhancers	Fetal Heart	heart
22	chr9:71555400-71560800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:71555600-71558000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:71555800-71558000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:71556200-71558000	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr9:71556400-71562000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:71556600-71558000	Genic enhancers	GM12878-XiMat	blood
28	chr9:71556600-71558200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:71556600-71558200	Strong transcription	Fetal Intestine Small	intestine
30	chr9:71556600-71566600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr9:71556800-71558000	Enhancers	Right Ventricle	heart
32	chr9:71557000-71558200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:71557200-71558400	Enhancers	Left Ventricle	heart
34	chr9:71557200-71558400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:71557400-71558000	Enhancers	H9 Cell Line	embryonic stem cell
36	chr9:71557400-71558200	Strong transcription	Colonic Mucosa	Colon
37	chr9:71557400-71566400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:71557600-71559400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr9:71557600-71578400	Weak transcription	HepG2	liver

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