Variant report

Variant	rs73364567
Chromosome Location	chr6:4848177-4848178
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4847558..4849642-chr6:4852103..4854411,2	K562	blood:
2	chr6:4776573..4778136-chr6:4847031..4849578,2	K562	blood:
3	chr6:4845889..4847519-chr6:4848149..4850482,2	MCF-7	breast:
4	chr6:4840303..4841822-chr6:4847282..4849004,2	MCF-7	breast:
5	chr6:4847745..4850576-chr6:4852287..4854812,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPP1R3G-4	chr6:4847760-4848591	NONHSAT107490

Variant related genes	Relation type
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13199417	0.81[ASN][1000 genomes]
rs13212871	0.81[ASN][1000 genomes]
rs1557032	1.00[EUR][1000 genomes]
rs17138859	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17138931	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17138959	0.87[EUR][1000 genomes]
rs17138966	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2235429	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2326553	0.81[ASN][1000 genomes]
rs4376391	1.00[EUR][1000 genomes]
rs56278978	1.00[EUR][1000 genomes]
rs58368827	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60609172	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60949901	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61278797	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6916304	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6916467	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6919412	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73348319	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73348345	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73348361	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73362530	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73362564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73364523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73364571	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743735	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7768749	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs811251	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs947151	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9502239	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9502244	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9502247	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9502248	1.00[EUR][1000 genomes]
rs9502249	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9502250	0.81[ASN][1000 genomes]
rs9502251	0.87[EUR][1000 genomes]
rs9504262	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9504267	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9504269	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9504270	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504271	1.00[EUR][1000 genomes]
rs9504275	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9504276	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9504281	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9504284	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9504286	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription 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	10 gene(s)	inside rSNPs	diseases
2	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS 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
3	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1015888	chr6:4787784-4883663	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv966675	chr6:4819733-4855009	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4821200-4853600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:4830000-4848800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:4836800-4848600	Weak transcription	Right Ventricle	heart
4	chr6:4837400-4848400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:4844600-4859600	Weak transcription	Spleen	Spleen
6	chr6:4844800-4853200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:4844800-4854000	Weak transcription	NHEK	skin
8	chr6:4844800-4856600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:4844800-4863000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:4845000-4848800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:4845000-4849400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:4846000-4849200	Enhancers	Psoas Muscle	Psoas
13	chr6:4846200-4848600	Weak transcription	HSMMtube	muscle
14	chr6:4846400-4850600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:4846400-4859000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:4846800-4849000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:4847000-4848400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:4847000-4849000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:4847200-4849200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:4847200-4849200	Enhancers	Ovary	ovary
21	chr6:4847400-4848600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:4847400-4848600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:4847400-4848600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:4847400-4848800	Weak transcription	Liver	Liver
25	chr6:4847400-4848800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:4847400-4849200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr6:4847400-4854000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:4847400-4871000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:4847600-4848400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:4847600-4848600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:4847600-4848600	Weak transcription	Gastric	stomach
32	chr6:4847600-4848600	Weak transcription	Left Ventricle	heart
33	chr6:4847600-4848600	Weak transcription	Right Atrium	heart
34	chr6:4847600-4848800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:4847600-4848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:4847600-4848800	Weak transcription	Pancreas	Pancrea
37	chr6:4847600-4849200	Enhancers	Brain Substantia Nigra	brain
38	chr6:4847600-4850000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr6:4847600-4853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:4847600-4853800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:4847600-4854000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr6:4847600-4854000	Weak transcription	Lung	lung
43	chr6:4847800-4848600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr6:4847800-4849000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr6:4847800-4849200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr6:4848000-4848400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:4848000-4848400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr6:4848000-4848600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:4848000-4848600	Enhancers	Aorta	Aorta
50	chr6:4848000-4850000	Enhancers	HUVEC	blood vessel

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