Variant report

Variant	rs2837004
Chromosome Location	chr21:40765511-40765512
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40684582..40688018-chr21:40762846..40766549,4	MCF-7	breast:
2	chr21:40752170..40754899-chr21:40764074..40766605,2	MCF-7	breast:
3	chr21:40757591..40761225-chr21:40763023..40767191,7	K562	blood:

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1060180	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs10775662	0.85[CHB][hapmap]
rs13051949	0.83[ASN][1000 genomes]
rs13230	0.83[ASN][1000 genomes]
rs1554933	0.96[YRI][hapmap]
rs2063999	0.92[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs2244352	1.00[ASW][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs2299741	0.83[ASN][1000 genomes]
rs2836990	0.92[YRI][hapmap]
rs2836994	0.83[CHB][hapmap]
rs2836995	0.92[CHB][hapmap];0.81[CHD][hapmap]
rs2836996	0.92[CHB][hapmap];1.00[YRI][hapmap]
rs2836997	0.92[CHB][hapmap]
rs2836998	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2836999	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2837000	0.83[ASN][1000 genomes]
rs2837001	0.83[ASN][1000 genomes]
rs2837002	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2837003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837005	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2837006	0.85[CHB][hapmap]
rs2837007	0.85[CHB][hapmap];0.83[TSI][hapmap]
rs2837008	0.85[CHB][hapmap]
rs3761372	0.96[YRI][hapmap]
rs3787923	0.83[ASN][1000 genomes]
rs3787924	0.83[ASN][1000 genomes]
rs3787925	0.81[JPT][hapmap]
rs3827209	0.81[JPT][hapmap]
rs4358205	0.81[JPT][hapmap]
rs4818035	0.81[ASN][1000 genomes]
rs4818036	0.80[ASN][1000 genomes]
rs6517547	0.85[CHB][hapmap]
rs7277386	0.81[JPT][hapmap]
rs8127431	0.81[JPT][hapmap]
rs8131718	0.83[ASN][1000 genomes]
rs9305674	0.83[ASN][1000 genomes]
rs975934	0.81[JPT][hapmap]
rs9974828	0.84[CHB][hapmap]
rs9975761	0.83[AFR][1000 genomes]
rs9979083	0.82[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1056452	chr21:40741893-40782587	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1063521	chr21:40747754-40790197	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs2837004	HMGN1	cis	lymphoblastoid	seeQTL
rs2837004	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2837004	WRB	cis	Esophagus Muscularis	GTEx
rs2837004	LCA5L	cis	Esophagus Muscularis	GTEx
rs2837004	HMGN1	cis	cerebellum	SCAN
rs2837004	LOC643790	trans	multi-tissue	Pritchard
rs2837004	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2837004	WRB	cis	Nerve Tibial	GTEx
rs2837004	LCA5L	cis	Thyroid	GTEx
rs2837004	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2837004	WRB	cis	cerebellum	SCAN
rs2837004	LCA5L	cis	Whole Blood	GTEx
rs2837004	WRB	cis	Adipose Subcutaneous	GTEx
rs2837004	WRB	cis	Artery Tibial	GTEx
rs2837004	WRB	cis	multi-tissue	Pritchard
rs2837004	LCA5L	cis	Nerve Tibial	GTEx
rs2837004	LCA5L	cis	lung	GTEx
rs2837004	WRB	cis	Whole Blood	GTEx
rs2837004	LCA5L	cis	Artery Tibial	GTEx
rs2837004	WRB	cis	Thyroid	GTEx
rs2837004	HMGN1	cis	multi-tissue	Pritchard
rs2837004	WRB	cis	parietal	SCAN
rs2837004	WRB	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40760600-40771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:40760800-40766400	Weak transcription	Fetal Kidney	kidney
3	chr21:40761000-40769800	Weak transcription	HMEC	breast
4	chr21:40761000-40777200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr21:40761000-40779200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr21:40761000-40782600	Weak transcription	Right Atrium	heart
7	chr21:40761200-40771200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr21:40761800-40768200	Strong transcription	Fetal Intestine Small	intestine
9	chr21:40762200-40768200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:40762200-40768800	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr21:40762200-40770400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr21:40762200-40770400	Strong transcription	Fetal Muscle Leg	muscle
13	chr21:40762200-40770600	Strong transcription	Fetal Brain Female	brain
14	chr21:40762200-40771400	Strong transcription	Fetal Stomach	stomach
15	chr21:40762400-40765800	Strong transcription	HepG2	liver
16	chr21:40762400-40766000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr21:40762400-40768000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr21:40762400-40768000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr21:40762400-40768200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr21:40762400-40768400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr21:40762400-40768800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr21:40762400-40769000	Strong transcription	Primary T cells from cord blood	blood
23	chr21:40762400-40770200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr21:40762400-40770400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr21:40762400-40770400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr21:40762400-40770400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr21:40762400-40770400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr21:40762400-40770400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr21:40762400-40770400	Strong transcription	Ovary	ovary
30	chr21:40762400-40770400	Strong transcription	Thymus	Thymus
31	chr21:40762400-40771000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr21:40762400-40771200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr21:40762600-40765800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:40762600-40767000	Strong transcription	Brain Angular Gyrus	brain
35	chr21:40762600-40767000	Strong transcription	Brain Substantia Nigra	brain
36	chr21:40762600-40767200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr21:40762600-40767400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr21:40762600-40767800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr21:40762600-40767800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr21:40762600-40767800	Strong transcription	Osteobl	bone
41	chr21:40762600-40768000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr21:40762600-40768200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr21:40762600-40768200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr21:40762600-40768200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr21:40762600-40768200	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr21:40762600-40768200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr21:40762600-40768200	Strong transcription	Dnd41	blood
48	chr21:40762600-40768800	Strong transcription	Gastric	stomach
49	chr21:40762600-40769000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr21:40762600-40769000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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