Variant report

Variant	rs56859781
Chromosome Location	chr16:81390339-81390340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81389850..81392744-chr16:81404140..81407123,3	K562	blood:
2	chr16:81346954..81352914-chr16:81389410..81396228,9	MCF-7	breast:
3	chr16:81388209..81391799-chr16:81392393..81395438,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260495	Chromatin interaction
ENSG00000261609	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1075352	0.93[AMR][1000 genomes]
rs1075353	0.93[AMR][1000 genomes]
rs11861054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11861072	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11861112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11861158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11861322	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11861886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11862082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11862778	0.94[AMR][1000 genomes]
rs11862805	0.94[AMR][1000 genomes]
rs11866294	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11866308	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11866327	1.00[AMR][1000 genomes]
rs11866374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11866407	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11866408	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11866700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16955014	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16955018	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16955027	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16955031	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16955040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16955059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16955067	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16955071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16955074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16955083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16955109	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16955113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16955120	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16955138	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955149	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16955164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16955173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2317129	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28560203	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28561847	0.87[AMR][1000 genomes]
rs28864156	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34684636	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3803653	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57928297	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58590084	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58594614	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59579335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59586584	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9925624	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9935105	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer 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 miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1061359	chr16:81349826-81471867	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv542992	chr16:81349826-81471867	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	esv1792674	chr16:81375316-81391868	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81353400-81390400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr16:81354200-81391600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr16:81379400-81410600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr16:81380600-81396200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:81381000-81392600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr16:81381200-81390400	Weak transcription	Brain Substantia Nigra	brain
7	chr16:81381200-81391000	Weak transcription	Osteobl	bone
8	chr16:81381200-81396000	Weak transcription	Right Ventricle	heart
9	chr16:81382200-81391400	Weak transcription	Fetal Heart	heart
10	chr16:81382400-81390400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr16:81382400-81390400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr16:81382400-81391400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr16:81382400-81396200	Weak transcription	Pancreas	Pancrea
14	chr16:81382400-81418400	Weak transcription	Small Intestine	intestine
15	chr16:81382600-81391400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr16:81382600-81391400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr16:81382600-81391400	Weak transcription	Brain Angular Gyrus	brain
18	chr16:81382600-81396000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr16:81382600-81398600	Weak transcription	Fetal Thymus	thymus
20	chr16:81382800-81390400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr16:81382800-81391400	Weak transcription	Thymus	Thymus
22	chr16:81383000-81391400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr16:81383000-81391400	Weak transcription	HSMM	muscle
24	chr16:81383000-81391400	Weak transcription	HUVEC	blood vessel
25	chr16:81383000-81395200	Weak transcription	Fetal Brain Female	brain
26	chr16:81383000-81395800	Weak transcription	Brain Germinal Matrix	brain
27	chr16:81383000-81396200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr16:81383200-81391400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr16:81383200-81396000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr16:81383400-81395800	Weak transcription	Colonic Mucosa	Colon
31	chr16:81383400-81398000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr16:81383600-81395400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr16:81383600-81398600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr16:81383800-81391400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr16:81383800-81396200	Weak transcription	Spleen	Spleen
36	chr16:81384000-81390400	Weak transcription	NHDF-Ad	bronchial
37	chr16:81384000-81395600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr16:81384000-81398400	Weak transcription	NH-A	brain
39	chr16:81384000-81404800	Weak transcription	Stomach Mucosa	stomach
40	chr16:81384000-81410600	Weak transcription	Fetal Kidney	kidney
41	chr16:81384200-81434600	Weak transcription	NHLF	lung
42	chr16:81384200-81437400	Weak transcription	Fetal Brain Male	brain
43	chr16:81384400-81390400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr16:81385000-81406200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr16:81385400-81391400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr16:81385400-81391400	Weak transcription	Colon Smooth Muscle	Colon
47	chr16:81385400-81410800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr16:81385600-81418200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr16:81385800-81396000	Weak transcription	Brain Hippocampus Middle	brain
50	chr16:81385800-81399800	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links