Variant report

Variant	rs13097030
Chromosome Location	chr3:56603675-56603676
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	chr3:56595109..56597404-chr3:56602239..56604027,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10212341	0.90[YRI][hapmap]
rs10222449	0.88[EUR][1000 genomes]
rs10222462	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1045926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865998	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10866000	0.85[ASN][1000 genomes]
rs11130536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130538	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs11706624	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11715395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.88[ASN][1000 genomes]
rs11719656	0.81[ASN][1000 genomes]
rs11921326	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12488218	0.81[ASN][1000 genomes]
rs12490749	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12636392	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12636773	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715490	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094666	0.86[ASN][1000 genomes]
rs1352766	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1388251	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1491166	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17056878	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17216740	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2004199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2029464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2035798	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054988	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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2317133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2317245	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282533	0.83[CHB][hapmap]
rs28407059	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3732512	0.89[ASN][1000 genomes]
rs4093514	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681746	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs4681951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4681963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4974220	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974224	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66529035	0.81[ASN][1000 genomes]
rs6765870	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6774323	0.86[ASN][1000 genomes]
rs6784100	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6785479	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6790915	0.87[EUR][1000 genomes]
rs6798118	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6799576	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6802051	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6804262	0.84[ASN][1000 genomes]
rs6805469	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72877266	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7612599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7618024	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7626378	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629559	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7647272	0.88[EUR][1000 genomes]
rs9811046	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9820759	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs9822876	0.81[CHB][hapmap]
rs9836539	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9840528	0.95[CEU][hapmap];0.85[ASN][1000 genomes]
rs9842283	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9845096	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9845655	0.86[ASN][1000 genomes]
rs9846282	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9858728	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs9862490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9881005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881154	0.85[ASN][1000 genomes]
rs9881789	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9881961	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9985253	1.00[CEU][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9985254	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv3338042	chr3:56602712-56606910	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
4	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
6	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
7	chr3:56592600-56603800	Weak transcription	Stomach Mucosa	stomach
8	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
10	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:56594800-56604000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:56596000-56605800	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:56597200-56609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:56597400-56609400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:56597400-56610000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:56597600-56603800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:56597600-56605400	Strong transcription	Hela-S3	cervix
31	chr3:56597600-56608000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:56597800-56603800	Strong transcription	NH-A	brain
33	chr3:56597800-56607600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:56598000-56607000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:56598000-56607800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:56598000-56609200	Strong transcription	Fetal Thymus	thymus
37	chr3:56598000-56609800	Strong transcription	Primary T cells from cord blood	blood
38	chr3:56598600-56608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:56598600-56609600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:56598800-56607600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:56599600-56606000	Strong transcription	Thymus	Thymus
42	chr3:56599600-56606200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:56599800-56606000	Strong transcription	Fetal Stomach	stomach
44	chr3:56599800-56606200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:56599800-56607800	Strong transcription	Fetal Lung	lung
46	chr3:56599800-56608000	Strong transcription	Liver	Liver
47	chr3:56600000-56603800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:56600000-56604000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:56600000-56604000	Strong transcription	NHEK	skin
50	chr3:56600000-56604200	Strong transcription	Colonic Mucosa	Colon

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