Variant report

Variant	rs1887240
Chromosome Location	chr1:46881775-46881776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10252	0.81[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs11211271	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs12073998	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12075550	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs12563610	0.80[CHB][hapmap];1.00[MEX][hapmap]
rs324416	0.85[ASN][1000 genomes]
rs3863641	0.85[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs45564237	0.85[ASN][1000 genomes]
rs45577432	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4660345	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap]
rs4660925	0.81[ASN][1000 genomes]
rs873978	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs913168	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs9865	0.80[CHB][hapmap];0.81[CHD][hapmap]

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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46868000-46884200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:46868200-46883800	Weak transcription	HepG2	liver
3	chr1:46869000-46882000	Strong transcription	Fetal Intestine Small	intestine
4	chr1:46872200-46884800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:46872800-46882400	Weak transcription	Ovary	ovary
6	chr1:46872800-46882400	Weak transcription	Right Ventricle	heart
7	chr1:46872800-46908000	Weak transcription	Right Atrium	heart
8	chr1:46874800-46881800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:46875000-46882000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:46875200-46887800	Weak transcription	Stomach Mucosa	stomach
11	chr1:46876000-46882600	Weak transcription	Primary T cells from cord blood	blood
12	chr1:46877000-46884000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:46877400-46884800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:46878800-46882600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:46879000-46881800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:46879000-46882000	Strong transcription	Brain Anterior Caudate	brain
17	chr1:46879000-46886400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:46879400-46883200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:46879400-46883200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:46879400-46884800	Weak transcription	Placenta	Placenta
21	chr1:46879400-46888400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:46879800-46882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:46879800-46882400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:46879800-46882800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:46879800-46884200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:46880000-46881800	Strong transcription	Brain Hippocampus Middle	brain
27	chr1:46880000-46881800	Weak transcription	Thymus	Thymus
28	chr1:46880000-46882600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:46880000-46883000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:46880000-46883400	Weak transcription	Adipose Nuclei	Adipose
31	chr1:46880000-46886000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:46880000-46886400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:46880200-46883200	Weak transcription	Aorta	Aorta
34	chr1:46880200-46883200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:46880200-46883600	Weak transcription	Brain Germinal Matrix	brain
36	chr1:46880200-46885000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:46880400-46882800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:46880400-46883000	Weak transcription	Esophagus	oesophagus
39	chr1:46880400-46883600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr1:46880400-46884000	Weak transcription	Liver	Liver
41	chr1:46880400-46884000	Weak transcription	Fetal Brain Female	brain
42	chr1:46880400-46884200	Weak transcription	Fetal Intestine Large	intestine
43	chr1:46880400-46884800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr1:46880400-46885000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:46880400-46885000	Weak transcription	Spleen	Spleen
46	chr1:46880600-46886200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:46881200-46881800	Strong transcription	Pancreas	Pancrea
48	chr1:46881200-46885400	Weak transcription	Colonic Mucosa	Colon
49	chr1:46881400-46881800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:46881400-46881800	Strong transcription	Gastric	stomach

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