Variant report

Variant	rs73409577
Chromosome Location	chr15:42545037-42545038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42544904..42547005-chr15:42561537..42563318,2	K562	blood:
2	chr15:42544015..42546634-chr15:42547457..42549970,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs12437600	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12438240	0.83[EUR][1000 genomes]
rs12438369	0.81[ASN][1000 genomes]
rs12438509	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12440087	0.97[ASN][1000 genomes]
rs12441016	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12441642	0.81[ASN][1000 genomes]
rs16972779	0.85[AMR][1000 genomes]
rs16972887	0.97[ASN][1000 genomes]
rs16973008	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16973045	0.94[ASN][1000 genomes]
rs16973060	0.92[ASN][1000 genomes]
rs2138831	0.84[ASN][1000 genomes]
rs2407707	0.87[ASN][1000 genomes]
rs2412688	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28364388	0.81[ASN][1000 genomes]
rs28364393	1.00[EUR][1000 genomes]
rs28745877	0.83[EUR][1000 genomes]
rs3736099	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3743005	0.92[ASN][1000 genomes]
rs3743007	0.92[ASN][1000 genomes]
rs3743008	0.92[ASN][1000 genomes]
rs3825785	0.92[ASN][1000 genomes]
rs4506867	0.92[ASN][1000 genomes]
rs4923932	0.86[ASN][1000 genomes]
rs4923945	0.92[ASN][1000 genomes]
rs4924627	0.86[ASN][1000 genomes]
rs4924630	0.86[ASN][1000 genomes]
rs4924631	0.84[ASN][1000 genomes]
rs4924644	0.97[ASN][1000 genomes]
rs4924672	0.92[ASN][1000 genomes]
rs4924673	0.92[ASN][1000 genomes]
rs4924674	0.81[ASN][1000 genomes]
rs4924677	0.83[EUR][1000 genomes]
rs55671734	0.83[EUR][1000 genomes]
rs55882551	0.97[ASN][1000 genomes]
rs56257215	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56670003	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56702977	0.81[ASN][1000 genomes]
rs56987883	0.92[ASN][1000 genomes]
rs57134130	0.81[ASN][1000 genomes]
rs57393446	0.86[ASN][1000 genomes]
rs57933952	0.97[ASN][1000 genomes]
rs57973092	0.92[ASN][1000 genomes]
rs57976413	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58292736	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58313689	0.89[ASN][1000 genomes]
rs58712370	0.92[ASN][1000 genomes]
rs59094161	0.92[ASN][1000 genomes]
rs59132828	0.92[ASN][1000 genomes]
rs59138723	0.97[ASN][1000 genomes]
rs59320762	0.92[ASN][1000 genomes]
rs59893734	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59974698	0.97[ASN][1000 genomes]
rs60443443	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60634548	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61069354	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61133768	0.92[ASN][1000 genomes]
rs6493033	0.97[ASN][1000 genomes]
rs7179203	0.92[ASN][1000 genomes]
rs7180279	0.92[ASN][1000 genomes]
rs7180315	0.83[EUR][1000 genomes]
rs7181979	0.86[ASN][1000 genomes]
rs73398938	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73400993	0.87[ASN][1000 genomes]
rs73402707	0.92[ASN][1000 genomes]
rs73402745	0.83[EUR][1000 genomes]
rs73403365	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73407403	0.86[ASN][1000 genomes]
rs73407407	0.86[ASN][1000 genomes]
rs73407488	0.97[ASN][1000 genomes]
rs8025601	0.92[ASN][1000 genomes]
rs8027016	0.97[ASN][1000 genomes]
rs8041951	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking 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 miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1799961	chr15:42522773-42545863	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv1832380	chr15:42522773-42545863	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
2	chr15:42519400-42562800	Weak transcription	Fetal Heart	heart
3	chr15:42520200-42561000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:42521000-42551000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:42527200-42548200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:42528800-42548800	Weak transcription	Small Intestine	intestine
7	chr15:42529800-42548400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:42530200-42546400	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:42530600-42548800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:42530800-42551600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:42530800-42551600	Weak transcription	Right Ventricle	heart
12	chr15:42531800-42551800	Weak transcription	Psoas Muscle	Psoas
13	chr15:42532000-42551600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:42532200-42545600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:42532200-42551000	Weak transcription	HMEC	breast
16	chr15:42532200-42552800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:42532400-42548200	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:42532400-42548400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:42534800-42545400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:42534800-42548400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:42535200-42545600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:42535200-42546400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:42536600-42546600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:42542400-42547200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:42542800-42545800	ZNF genes & repeats	Fetal Brain Female	brain
26	chr15:42542800-42546000	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr15:42542800-42547600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:42542800-42550000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:42542800-42561600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:42543400-42545200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr15:42543400-42545200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:42543400-42545800	ZNF genes & repeats	Brain Germinal Matrix	brain
33	chr15:42543400-42546200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:42543400-42547800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr15:42543400-42551000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
36	chr15:42543400-42559000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:42543400-42561200	Strong transcription	Liver	Liver
38	chr15:42543600-42545800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr15:42543600-42547600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
40	chr15:42543600-42548600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
41	chr15:42543600-42552600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:42543600-42561000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:42543800-42545600	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr15:42543800-42545800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:42543800-42545800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:42543800-42545800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
47	chr15:42543800-42545800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr15:42543800-42545800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:42543800-42545800	ZNF genes & repeats	Fetal Intestine Large	intestine
50	chr15:42543800-42545800	ZNF genes & repeats	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links