Variant report

Variant	rs6560398
Chromosome Location	chr9:71472092-71472093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10115536	0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10117946	0.81[ASN][1000 genomes]
rs10781232	0.83[CHB][hapmap];0.92[ASN][1000 genomes]
rs10869404	0.92[ASN][1000 genomes]
rs11143802	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs12684346	0.82[CEU][hapmap]
rs12686613	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12686693	0.82[CEU][hapmap]
rs1412988	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1414946	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1537887	0.94[ASN][1000 genomes]
rs17057642	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs17057918	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs17058884	0.82[CEU][hapmap]
rs17081050	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17081071	0.82[CEU][hapmap]
rs1889937	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2027024	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2039425	0.87[ASN][1000 genomes]
rs2039625	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2151421	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2151422	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3750377	0.80[ASN][1000 genomes]
rs4237268	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs4259475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4745321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4745351	0.97[ASN][1000 genomes]
rs4745354	0.95[ASN][1000 genomes]
rs4745359	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs61196668	0.95[ASN][1000 genomes]
rs6560407	0.95[ASN][1000 genomes]
rs7019684	0.84[ASN][1000 genomes]
rs7032651	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7035999	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs7039817	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs7041004	0.85[CEU][hapmap]
rs7045163	0.95[ASN][1000 genomes]
rs7046065	0.95[ASN][1000 genomes]
rs7046284	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs72512921	0.81[ASN][1000 genomes]
rs7851399	0.90[ASN][1000 genomes]
rs7861710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7865412	0.86[ASN][1000 genomes]
rs7869452	0.86[ASN][1000 genomes]
rs975123	0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.80[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:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71438000-71491200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:71441000-71478600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:71448200-71485600	Weak transcription	Stomach Mucosa	stomach
4	chr9:71459000-71519200	Weak transcription	Colonic Mucosa	Colon
5	chr9:71459400-71480000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr9:71459800-71478600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr9:71460400-71495600	Weak transcription	Aorta	Aorta
8	chr9:71460600-71473800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr9:71460800-71517000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr9:71463400-71492800	Weak transcription	GM12878-XiMat	blood
11	chr9:71463600-71501800	Weak transcription	Small Intestine	intestine
12	chr9:71465800-71480200	Weak transcription	HepG2	liver
13	chr9:71466800-71478800	Weak transcription	Fetal Intestine Large	intestine
14	chr9:71467800-71495800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:71468200-71486600	Weak transcription	Left Ventricle	heart
16	chr9:71469400-71472200	Weak transcription	Fetal Intestine Small	intestine
17	chr9:71470600-71483600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:71471000-71474600	Strong transcription	Primary B cells from cord blood	blood
19	chr9:71471200-71478600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:71471400-71474400	Weak transcription	Right Atrium	heart
21	chr9:71471600-71474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:71471800-71472200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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