Variant report

Variant	rs59893734
Chromosome Location	chr15:42504769-42504770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42503423..42505275-chr15:42506860..42509777,2	K562	blood:
2	chr15:42503775..42505358-chr15:42508277..42510017,2	K562	blood:
3	chr15:42499311..42503091-chr15:42504609..42507000,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166887	Chromatin interaction
ENSG00000261002	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12437600	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12438509	0.89[ASN][1000 genomes]
rs12440087	0.89[ASN][1000 genomes]
rs12441016	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12441642	0.95[ASN][1000 genomes]
rs16972779	0.84[ASN][1000 genomes]
rs16972887	0.89[ASN][1000 genomes]
rs16973008	0.89[ASN][1000 genomes]
rs16973045	0.86[ASN][1000 genomes]
rs16973060	0.83[ASN][1000 genomes]
rs2138831	0.97[ASN][1000 genomes]
rs2412688	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28364393	1.00[EUR][1000 genomes]
rs28745877	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3736099	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743005	0.83[ASN][1000 genomes]
rs3743007	0.83[ASN][1000 genomes]
rs3743008	0.83[ASN][1000 genomes]
rs3825785	0.83[ASN][1000 genomes]
rs4506867	0.83[ASN][1000 genomes]
rs4923932	1.00[ASN][1000 genomes]
rs4923945	0.83[ASN][1000 genomes]
rs4924627	1.00[ASN][1000 genomes]
rs4924628	1.00[AFR][1000 genomes]
rs4924630	1.00[ASN][1000 genomes]
rs4924631	0.97[ASN][1000 genomes]
rs4924644	0.89[ASN][1000 genomes]
rs4924672	0.83[ASN][1000 genomes]
rs4924673	0.83[ASN][1000 genomes]
rs55882551	0.89[ASN][1000 genomes]
rs56257215	0.89[ASN][1000 genomes]
rs56670003	0.89[ASN][1000 genomes]
rs56987883	0.83[ASN][1000 genomes]
rs57393446	1.00[ASN][1000 genomes]
rs57933952	0.89[ASN][1000 genomes]
rs57973092	0.83[ASN][1000 genomes]
rs57976413	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58292736	0.89[ASN][1000 genomes]
rs58313689	0.81[ASN][1000 genomes]
rs58712370	0.83[ASN][1000 genomes]
rs59094161	0.83[ASN][1000 genomes]
rs59132828	0.84[ASN][1000 genomes]
rs59138723	0.89[ASN][1000 genomes]
rs59320762	0.83[ASN][1000 genomes]
rs59974698	0.89[ASN][1000 genomes]
rs60443443	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60634548	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61069354	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61133768	0.83[ASN][1000 genomes]
rs6493033	0.89[ASN][1000 genomes]
rs7179203	0.83[ASN][1000 genomes]
rs7180279	0.83[ASN][1000 genomes]
rs7181979	1.00[ASN][1000 genomes]
rs73398938	0.89[ASN][1000 genomes]
rs73402707	0.83[ASN][1000 genomes]
rs73403365	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73407403	1.00[ASN][1000 genomes]
rs73407407	1.00[ASN][1000 genomes]
rs73407488	0.89[ASN][1000 genomes]
rs73409577	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8025601	0.84[ASN][1000 genomes]
rs8027016	0.89[ASN][1000 genomes]
rs8041951	0.83[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	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	nsv1054102	chr15:42493052-42528765	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42500600-42505200	Weak transcription	Spleen	Spleen
2	chr15:42500600-42513800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
4	chr15:42501000-42505000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:42501000-42505200	Weak transcription	Fetal Brain Male	brain
6	chr15:42501000-42508400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:42501000-42510200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:42501000-42510400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:42501000-42510800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:42501000-42511000	Weak transcription	Colonic Mucosa	Colon
11	chr15:42501000-42512600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:42501000-42512800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:42501000-42513600	Strong transcription	HSMM	muscle
14	chr15:42501000-42518600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:42501000-42518800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:42501000-42520800	Weak transcription	Psoas Muscle	Psoas
17	chr15:42501000-42534800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:42501000-42536600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:42501000-42536800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:42501000-42538000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:42501200-42505000	Weak transcription	Fetal Intestine Small	intestine
22	chr15:42501200-42505400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:42501200-42505600	Strong transcription	NHLF	lung
24	chr15:42501200-42506000	Strong transcription	GM12878-XiMat	blood
25	chr15:42501200-42513000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:42501200-42514200	Weak transcription	Right Ventricle	heart
27	chr15:42501200-42514600	Weak transcription	Pancreas	Pancrea
28	chr15:42501200-42523200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:42501200-42532400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr15:42501400-42504800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr15:42501400-42506000	Strong transcription	Placenta	Placenta
32	chr15:42501400-42508200	Strong transcription	HSMMtube	muscle
33	chr15:42501400-42512600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:42501400-42512800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:42501400-42513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:42501600-42505800	Strong transcription	NHEK	skin
37	chr15:42501600-42506000	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr15:42501600-42507000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:42501600-42512600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr15:42501600-42512800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:42501600-42513000	Strong transcription	Liver	Liver
42	chr15:42501800-42536800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:42502000-42505000	Strong transcription	HMEC	breast
44	chr15:42502000-42505200	Strong transcription	Brain Hippocampus Middle	brain
45	chr15:42502000-42505800	Strong transcription	Fetal Brain Female	brain
46	chr15:42502000-42507000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr15:42502000-42511400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr15:42502000-42512600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr15:42502000-42512800	Strong transcription	Osteobl	bone
50	chr15:42502000-42521200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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