Variant report

Variant	rs1175643
Chromosome Location	chr1:112979042-112979043
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1175624	0.96[AFR][1000 genomes]
rs1175627	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1175628	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175637	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175639	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1175640	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175642	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175644	0.87[AFR][1000 genomes]
rs1759691	0.87[AFR][1000 genomes]
rs1777621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2483347	1.00[AFR][1000 genomes]
rs2780274	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2780276	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2798246	0.88[AFR][1000 genomes];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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1850997	chr1:112944472-112993754	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112942400-112988200	Weak transcription	Small Intestine	intestine
2	chr1:112947200-112981000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:112952400-112990600	Weak transcription	Esophagus	oesophagus
4	chr1:112952600-112981400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:112957400-112986600	Weak transcription	NHLF	lung
6	chr1:112957600-112997600	Weak transcription	Brain Anterior Caudate	brain
7	chr1:112959600-112991600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:112959800-112992800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:112960000-112980800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:112960000-112981600	Weak transcription	Liver	Liver
11	chr1:112960000-112995200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:112960000-112996800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:112960200-112981200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:112960200-112991600	Weak transcription	Hela-S3	cervix
15	chr1:112960400-112991400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:112961200-112995600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:112961400-112980600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:112961600-112981200	Weak transcription	Fetal Brain Female	brain
19	chr1:112961800-112986800	Weak transcription	HMEC	breast
20	chr1:112962000-112979600	Weak transcription	Fetal Kidney	kidney
21	chr1:112962000-112990800	Weak transcription	Fetal Brain Male	brain
22	chr1:112962600-112990400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:112962600-112991600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:112964000-112982200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:112965800-112980400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:112965800-112983200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:112965800-112986400	Weak transcription	NHDF-Ad	bronchial
28	chr1:112965800-112996200	Weak transcription	Placenta	Placenta
29	chr1:112967000-112991600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:112967800-112982200	Weak transcription	HSMMtube	muscle
31	chr1:112968600-112981200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:112968600-112986600	Weak transcription	NHEK	skin
33	chr1:112968600-112987400	Weak transcription	Fetal Intestine Large	intestine
34	chr1:112968600-112987600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:112968600-112990600	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:112968600-112994800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:112968600-112995400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:112968600-112995600	Weak transcription	Colonic Mucosa	Colon
39	chr1:112969600-112981200	Weak transcription	Fetal Stomach	stomach
40	chr1:112971800-112979800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:112972000-112980600	Weak transcription	Fetal Lung	lung
42	chr1:112972200-112991400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:112973400-112985400	Weak transcription	Left Ventricle	heart
44	chr1:112973600-112980400	Weak transcription	Ovary	ovary
45	chr1:112973600-112988800	Weak transcription	Lung	lung
46	chr1:112974000-112979400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:112974000-112997000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:112974200-112979400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:112974200-112979600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:112974400-112980800	Weak transcription	Adipose Nuclei	Adipose

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