Variant report

Variant	rs1258021
Chromosome Location	chr1:47059934-47059935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11541308	1.00[AMR][1000 genomes]
rs1258007	0.87[AFR][1000 genomes]
rs1258011	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1258016	1.00[ASW][hapmap]
rs1258018	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1258019	0.87[AFR][1000 genomes]
rs2476167	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active 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
5	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47023200-47060000	Strong transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:47025600-47062400	Weak transcription	Fetal Heart	heart
3	chr1:47036000-47060000	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr1:47039200-47060400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:47039600-47060000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:47040200-47060400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:47042600-47060400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr1:47042600-47069000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:47042800-47068800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:47045600-47068800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:47046200-47069000	Weak transcription	Fetal Kidney	kidney
12	chr1:47047800-47060000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:47048400-47069000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:47049600-47060400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:47050600-47068600	Weak transcription	NHDF-Ad	bronchial
16	chr1:47051000-47061000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:47052200-47060000	Strong transcription	Liver	Liver
18	chr1:47052200-47060000	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:47052400-47060000	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:47053200-47060200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:47054400-47060000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:47054400-47060000	Strong transcription	Fetal Thymus	thymus
23	chr1:47054400-47060000	Strong transcription	Lung	lung
24	chr1:47054400-47060000	Strong transcription	Thymus	Thymus
25	chr1:47054600-47060000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:47054600-47060000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:47054600-47060000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:47054600-47060000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:47054600-47060000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr1:47054600-47060000	Strong transcription	Fetal Intestine Small	intestine
31	chr1:47054600-47060000	Strong transcription	Fetal Stomach	stomach
32	chr1:47054600-47060000	Strong transcription	Left Ventricle	heart
33	chr1:47054600-47060000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr1:47054600-47060000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:47054600-47060200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:47054600-47060200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:47054600-47060400	Strong transcription	NHEK	skin
38	chr1:47054800-47060000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:47054800-47060000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:47054800-47060200	Strong transcription	Fetal Intestine Large	intestine
41	chr1:47054800-47060600	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:47055000-47060200	Strong transcription	Osteobl	bone
43	chr1:47055000-47060800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:47055400-47060000	Strong transcription	GM12878-XiMat	blood
45	chr1:47055400-47068800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:47055600-47060000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:47055800-47060000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:47056000-47060600	Strong transcription	Pancreas	Pancrea
49	chr1:47056400-47067000	Weak transcription	Stomach Mucosa	stomach
50	chr1:47056600-47060000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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