Variant report

Variant	rs338242
Chromosome Location	chr1:58933918-58933919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:58920454..58922828-chr1:58933133..58935676,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TACSTD2-3	chr1:58933599-58934677	NONHSAT003505

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs338236	1.00[AMR][1000 genomes]
rs338249	1.00[AMR][1000 genomes]
rs706460	1.00[AMR][1000 genomes]
rs843988	1.00[AMR][1000 genomes]
rs849588	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv829948	chr1:58803681-58971380	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv546314	chr1:58915624-58936384	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58899000-58934200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:58918400-58974000	Weak transcription	Spleen	Spleen
3	chr1:58920400-58934000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:58923200-58954200	Weak transcription	Pancreas	Pancrea
5	chr1:58925000-58942400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:58926400-58942800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:58927400-58934000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:58927400-58943200	Weak transcription	Primary B cells from cord blood	blood
9	chr1:58928600-58945800	Weak transcription	Aorta	Aorta
10	chr1:58929000-58954600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:58929800-58934200	Weak transcription	Lung	lung
12	chr1:58930400-58945800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:58930400-58949400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:58930800-58934000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:58931000-58954200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:58931000-58954600	Weak transcription	Fetal Intestine Large	intestine
17	chr1:58931000-58954800	Weak transcription	Gastric	stomach
18	chr1:58931000-58977000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:58931200-58934000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:58931200-58952600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:58931200-58969400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:58931600-58974000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:58932000-58934800	Strong transcription	Ovary	ovary
25	chr1:58932000-58935600	Weak transcription	Colonic Mucosa	Colon
26	chr1:58932200-58945800	Weak transcription	Adipose Nuclei	Adipose
27	chr1:58932400-58934000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:58932400-58934000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:58932400-58934000	Weak transcription	HSMM	muscle
30	chr1:58932400-58947400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:58932600-58934000	Weak transcription	Primary T cells from cord blood	blood
32	chr1:58932600-58934200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:58932600-58934200	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:58932600-58946000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:58932600-58947400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:58932600-58947600	Weak transcription	Dnd41	blood
37	chr1:58932600-58948400	Weak transcription	Fetal Stomach	stomach
38	chr1:58932600-58954600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:58932600-58974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:58932600-58977000	Weak transcription	HSMMtube	muscle
41	chr1:58932800-58934000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:58932800-58934000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:58932800-58934200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:58932800-58954000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:58932800-58954200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:58932800-58968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:58933000-58934000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:58933000-58934200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:58933000-58934200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:58933000-58934200	Weak transcription	Left Ventricle	heart

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