Variant report

Variant	rs873978
Chromosome Location	chr1:46873903-46873904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46873304..46875119-chr1:46884031..46886700,3	K562	blood:
2	chr1:46873630..46874449-chr1:47191463..47192117,2	K562	blood:
3	chr1:46859846..46861376-chr1:46873214..46876105,2	MCF-7	breast:
4	chr1:46871688..46875401-chr1:47182655..47185240,3	K562	blood:

Variant related genes	Relation type
ENSG00000117480	Chromatin interaction
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10252	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs11211271	0.82[JPT][hapmap]
rs12073998	0.81[JPT][hapmap]
rs12075550	0.82[JPT][hapmap]
rs12563610	0.80[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs1887240	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs324416	0.96[ASN][1000 genomes]
rs3863641	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs3891758	0.84[ASN][1000 genomes]
rs4110477	0.82[ASN][1000 genomes]
rs41294484	0.83[ASN][1000 genomes]
rs45480993	0.87[ASN][1000 genomes]
rs45540335	0.87[ASN][1000 genomes]
rs45564237	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45577432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4660345	0.80[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs4660925	0.80[ASN][1000 genomes]
rs58710660	0.86[ASN][1000 genomes]
rs59082884	0.83[ASN][1000 genomes]
rs60519942	0.86[ASN][1000 genomes]
rs61221162	0.83[ASN][1000 genomes]
rs913168	0.88[JPT][hapmap]
rs9865	0.80[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.83[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	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	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46861000-46874400	Weak transcription	Primary T cells from cord blood	blood
2	chr1:46861200-46879000	Weak transcription	Aorta	Aorta
3	chr1:46861200-46879400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:46861600-46880400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:46865400-46876000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:46867800-46877000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:46868000-46876200	Weak transcription	Small Intestine	intestine
8	chr1:46868000-46884200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:46868200-46875000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:46868200-46883800	Weak transcription	HepG2	liver
11	chr1:46869000-46882000	Strong transcription	Fetal Intestine Small	intestine
12	chr1:46870200-46874000	Enhancers	K562	blood
13	chr1:46871800-46874400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:46871800-46875200	Enhancers	Placenta	Placenta
15	chr1:46872200-46874000	Weak transcription	Esophagus	oesophagus
16	chr1:46872200-46874200	Weak transcription	Lung	lung
17	chr1:46872200-46875000	Enhancers	HSMM	muscle
18	chr1:46872200-46876400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:46872200-46880200	Strong transcription	Pancreas	Pancrea
20	chr1:46872200-46884800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:46872400-46876400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:46872600-46880400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:46872800-46874200	Weak transcription	Spleen	Spleen
24	chr1:46872800-46874400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:46872800-46876200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:46872800-46878400	Weak transcription	Left Ventricle	heart
27	chr1:46872800-46880400	Strong transcription	Liver	Liver
28	chr1:46872800-46880400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:46872800-46880400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:46872800-46882400	Weak transcription	Ovary	ovary
31	chr1:46872800-46882400	Weak transcription	Right Ventricle	heart
32	chr1:46872800-46908000	Weak transcription	Right Atrium	heart
33	chr1:46873000-46874000	Weak transcription	Fetal Brain Female	brain
34	chr1:46873000-46874200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:46873000-46874200	Weak transcription	Adipose Nuclei	Adipose
36	chr1:46873000-46875600	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:46873000-46877800	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr1:46873000-46880600	Strong transcription	Gastric	stomach
39	chr1:46873000-46880800	Weak transcription	Fetal Thymus	thymus
40	chr1:46873000-46881000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:46873200-46874200	Weak transcription	Brain Germinal Matrix	brain
42	chr1:46873200-46874200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:46873200-46874200	Weak transcription	Fetal Stomach	stomach
44	chr1:46873200-46874400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:46873200-46875400	Weak transcription	Fetal Kidney	kidney
46	chr1:46873200-46875600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:46873200-46876200	Strong transcription	Brain Anterior Caudate	brain
48	chr1:46873200-46876400	Strong transcription	Fetal Intestine Large	intestine
49	chr1:46873200-46876600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:46873200-46878600	Strong transcription	Brain Cingulate Gyrus	brain

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