Variant report

Variant	rs17839374
Chromosome Location	chr5:42720307-42720308
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:42710379..42715980-chr5:42716772..42720517,5	K562	blood:
2	chr5:42714480..42717427-chr5:42718299..42720344,4	K562	blood:
3	chr5:42720219..42722168-chr5:42727317..42730144,2	K562	blood:
4	chr5:42718003..42720870-chr5:43094182..43097027,2	K562	blood:

Variant related genes	Relation type
ENSG00000270513	Chromatin interaction
ENSG00000112964	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10038477	0.82[ASN][1000 genomes]
rs10041130	0.97[ASN][1000 genomes]
rs10044169	0.82[ASN][1000 genomes]
rs10061833	0.82[ASN][1000 genomes]
rs10077296	0.82[ASN][1000 genomes]
rs10941583	0.91[ASN][1000 genomes]
rs12652476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654861	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12656017	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12658099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12658163	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1423655	0.94[ASN][1000 genomes]
rs16872680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872694	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16872762	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872830	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16872832	1.00[AMR][1000 genomes]
rs17839373	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230808	0.94[ASN][1000 genomes]
rs230809	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230811	0.91[ASN][1000 genomes]
rs2548719	0.89[ASN][1000 genomes]
rs28918068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28919894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28919901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28919903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28943887	1.00[EUR][1000 genomes]
rs28943888	1.00[EUR][1000 genomes]
rs2910854	0.94[ASN][1000 genomes]
rs2910860	0.94[ASN][1000 genomes]
rs2910863	0.94[ASN][1000 genomes]
rs2910866	0.94[ASN][1000 genomes]
rs2910878	0.82[ASN][1000 genomes]
rs2910879	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972752	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972764	0.81[ASN][1000 genomes]
rs2972768	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972769	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972780	0.82[ASN][1000 genomes]
rs2972782	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972995	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973004	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973008	0.89[ASN][1000 genomes]
rs2973009	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973016	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973019	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973030	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34319505	1.00[EUR][1000 genomes]
rs34382565	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35291899	0.85[ASN][1000 genomes]
rs35389780	1.00[EUR][1000 genomes]
rs35436563	1.00[EUR][1000 genomes]
rs35604733	1.00[ASN][1000 genomes]
rs4242119	0.82[ASN][1000 genomes]
rs4376276	0.92[ASN][1000 genomes]
rs4637559	0.92[ASN][1000 genomes]
rs4866947	0.82[ASN][1000 genomes]
rs4866948	0.82[ASN][1000 genomes]
rs6182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr5:42688400-42722200	Weak transcription	Pancreas	Pancrea
2	chr5:42706000-42720400	Weak transcription	Colon Smooth Muscle	Colon
3	chr5:42708800-42722800	Strong transcription	Liver	Liver
4	chr5:42714200-42721200	Weak transcription	Psoas Muscle	Psoas
5	chr5:42716600-42722000	Weak transcription	HSMMtube	muscle
6	chr5:42717400-42720600	Weak transcription	Fetal Kidney	kidney
7	chr5:42718000-42720400	Weak transcription	Brain Substantia Nigra	brain
8	chr5:42718000-42721000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:42718400-42722400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:42718400-42722400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:42718600-42720400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr5:42718600-42720800	Strong transcription	Adipose Nuclei	Adipose
13	chr5:42718600-42721000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr5:42718600-42721200	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:42718600-42721800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr5:42719200-42720400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:42719200-42720800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr5:42719200-42721400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:42719200-42721600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:42719400-42720400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:42719400-42720400	Weak transcription	Fetal Thymus	thymus
22	chr5:42719400-42720400	Weak transcription	Thymus	Thymus
23	chr5:42719400-42721600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:42719400-42723400	Weak transcription	Fetal Intestine Large	intestine
25	chr5:42719600-42720400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:42719600-42720400	Weak transcription	GM12878-XiMat	blood
27	chr5:42719600-42720600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:42719600-42721200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:42719600-42721200	Weak transcription	Ovary	ovary
30	chr5:42719600-42721200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:42719600-42721400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:42719600-42721600	Weak transcription	HSMM	muscle
33	chr5:42719600-42722000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:42719600-42722200	Weak transcription	Esophagus	oesophagus
35	chr5:42719600-42722200	Weak transcription	Spleen	Spleen
36	chr5:42719600-42722800	Weak transcription	Fetal Stomach	stomach
37	chr5:42719600-42723800	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:42719600-42723800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:42719600-42724000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:42719800-42720400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr5:42719800-42720400	Weak transcription	Aorta	Aorta
42	chr5:42719800-42720600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:42719800-42721400	Weak transcription	Osteobl	bone
44	chr5:42719800-42723800	Weak transcription	Fetal Lung	lung
45	chr5:42719800-42724200	Weak transcription	Left Ventricle	heart
46	chr5:42720000-42720600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr5:42720000-42720800	Enhancers	Primary T cells from cord blood	blood
48	chr5:42720200-42720600	Enhancers	Primary T cells fromperipheralblood	blood
49	chr5:42720200-42720800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:42720200-42721600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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