Variant report

Variant	rs3797247
Chromosome Location	chr5:53510482-53510483
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	chr5:53508333..53510735-chr5:53512429..53514270,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10052279	1.00[CHB][hapmap]
rs10055804	1.00[CHB][hapmap]
rs10057147	1.00[CHB][hapmap]
rs10065324	1.00[CHB][hapmap]
rs10079659	1.00[CHB][hapmap]
rs11953312	1.00[CHB][hapmap]
rs13358454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs13435967	1.00[CHB][hapmap]
rs156696	1.00[CHB][hapmap]
rs156832	1.00[CHB][hapmap]
rs157235	1.00[CHB][hapmap]
rs1645549	1.00[CHB][hapmap]
rs1664668	1.00[CHB][hapmap]
rs16882296	1.00[CHB][hapmap]
rs16882383	1.00[CHB][hapmap]
rs16882423	1.00[CHB][hapmap]
rs16882424	1.00[CHB][hapmap]
rs16882437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs16882447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs255678	1.00[CHB][hapmap]
rs25854	1.00[CHB][hapmap]
rs25859	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs25860	1.00[CHB][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs25861	0.83[EUR][1000 genomes]
rs27664	1.00[CHB][hapmap]
rs27677	1.00[CHB][hapmap]
rs277336	1.00[CHB][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs277337	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs277341	1.00[CHB][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs2783	1.00[CHB][hapmap]
rs33284	0.82[MEX][hapmap]
rs3776658	0.84[CEU][hapmap];0.85[LWK][hapmap];0.84[TSI][hapmap];0.82[AFR][1000 genomes]
rs3797246	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3797252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs3846490	1.00[CHB][hapmap]
rs4373242	1.00[CHB][hapmap]
rs57562307	0.98[EUR][1000 genomes]
rs59430615	0.98[EUR][1000 genomes]
rs640818	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs674377	0.83[EUR][1000 genomes]
rs675674	1.00[CHB][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs675745	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6865125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs6871446	1.00[CHB][hapmap]
rs6879693	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs6896006	1.00[CHB][hapmap]
rs7705101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[TSI][hapmap];0.98[EUR][1000 genomes]
rs7713087	1.00[CHB][hapmap]
rs7715885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs9292039	1.00[CHB][hapmap]
rs9292040	1.00[CHB][hapmap]

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	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
7	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
13	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
14	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
17	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
18	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
19	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv1031072	chr5:53490130-53698866	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53506000-53513200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:53506400-53511600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:53506800-53514400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr5:53507000-53512000	Weak transcription	A549	lung
5	chr5:53507200-53513400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:53507200-53513400	Weak transcription	Osteobl	bone
7	chr5:53507200-53518400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:53507200-53519600	Weak transcription	Left Ventricle	heart
9	chr5:53507400-53512000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:53507400-53512400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:53507800-53512600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr5:53508000-53511200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr5:53508000-53511200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr5:53508000-53513600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr5:53508200-53510800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:53508200-53513400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:53508200-53513800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:53508200-53514400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr5:53508200-53514400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr5:53508400-53510800	Weak transcription	Right Atrium	heart
21	chr5:53508400-53531200	Weak transcription	Gastric	stomach
22	chr5:53508800-53511000	Weak transcription	Aorta	Aorta
23	chr5:53508800-53513400	Weak transcription	NHLF	lung
24	chr5:53509200-53511800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr5:53509600-53511000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:53510000-53511000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr5:53510000-53511000	Enhancers	Placenta	Placenta
28	chr5:53510000-53512000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:53510000-53513800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:53510200-53510600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:53510200-53510600	Enhancers	Colon Smooth Muscle	Colon
32	chr5:53510200-53510800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:53510200-53510800	Enhancers	Right Ventricle	heart
34	chr5:53510200-53511000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr5:53510200-53511200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:53510200-53511400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:53510200-53511400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:53510200-53511400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr5:53510200-53512200	Enhancers	H9 Cell Line	embryonic stem cell
40	chr5:53510200-53512800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr5:53510400-53511400	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links