Variant report

Variant	rs2837007
Chromosome Location	chr21:40772484-40772485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40763849..40765895-chr21:40771181..40773683,2	MCF-7	breast:
2	chr21:40772342..40774461-chr21:40776080..40778844,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1060180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10775662	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11701047	0.82[EUR][1000 genomes]
rs13051571	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13051949	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13230	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094874	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2244352	0.80[CHD][hapmap]
rs2299739	0.83[EUR][1000 genomes]
rs2299741	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836994	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs2836995	0.92[CHB][hapmap]
rs2836996	0.92[CHB][hapmap]
rs2836997	0.82[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.84[EUR][1000 genomes]
rs2836998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837000	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837001	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837002	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837003	0.85[CHB][hapmap];0.83[TSI][hapmap]
rs2837004	0.85[CHB][hapmap];0.83[TSI][hapmap]
rs2837005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837006	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837008	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3787923	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3787924	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4816624	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs4818035	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4818036	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517547	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8131718	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9305674	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9974828	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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:28)

SNP	Gene	Cis/trans	Tissue	Source
rs2837007	LCA5L	cis	Esophagus Muscularis	GTEx
rs2837007	HMGN1	cis	multi-tissue	Pritchard
rs2837007	LCA5L	cis	Artery Aorta	GTEx
rs2837007	WRB	cis	multi-tissue	Pritchard
rs2837007	LCA5L	cis	Nerve Tibial	GTEx
rs2837007	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2837007	HMGN1	cis	lymphoblastoid	seeQTL
rs2837007	WRB	cis	Artery Tibial	GTEx
rs2837007	LCA5L	cis	Artery Tibial	GTEx
rs2837007	WRB	cis	lung	GTEx
rs2837007	WRB	cis	Whole Blood	GTEx
rs2837007	LCA5L	cis	Thyroid	GTEx
rs2837007	HMGN1	cis	cerebellum	SCAN
rs2837007	LCA5L	cis	lung	GTEx
rs2837007	WRB	cis	parietal	SCAN
rs2837007	LCA5L	cis	Whole Blood	GTEx
rs2837007	WRB	cis	cerebellum	SCAN
rs2837007	LOC643790	trans	multi-tissue	Pritchard
rs2837007	LCA5L	cis	Stomach	GTEx
rs2837007	WRB	cis	Esophagus Muscularis	GTEx
rs2837007	SH3BGR	cis	Adipose Subcutaneous	GTEx
rs2837007	WRB	cis	Thyroid	GTEx
rs2837007	WRB	cis	Nerve Tibial	GTEx
rs2837007	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2837007	LCA5L	cis	Esophagus Mucosa	GTEx
rs2837007	WRB	cis	Artery Aorta	GTEx
rs2837007	WRB	cis	Adipose Subcutaneous	GTEx
rs2837007	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40761000-40777200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:40761000-40779200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr21:40761000-40782600	Weak transcription	Right Atrium	heart
4	chr21:40762800-40773000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr21:40764600-40775200	Weak transcription	Small Intestine	intestine
6	chr21:40764600-40800600	Weak transcription	Psoas Muscle	Psoas
7	chr21:40764800-40773000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:40765200-40780400	Weak transcription	Stomach Mucosa	stomach
9	chr21:40765400-40777800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr21:40765400-40778000	Weak transcription	Colonic Mucosa	Colon
11	chr21:40765400-40778200	Weak transcription	Fetal Brain Male	brain
12	chr21:40765400-40779200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr21:40765400-40780000	Weak transcription	A549	lung
14	chr21:40765600-40777800	Weak transcription	Pancreas	Pancrea
15	chr21:40765600-40778000	Weak transcription	NH-A	brain
16	chr21:40765600-40781200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr21:40765800-40777400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr21:40765800-40777800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr21:40765800-40778000	Weak transcription	HSMM	muscle
20	chr21:40766800-40776200	Weak transcription	K562	blood
21	chr21:40766800-40777200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr21:40766800-40777800	Weak transcription	NHDF-Ad	bronchial
23	chr21:40766800-40778000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr21:40766800-40779000	Weak transcription	Right Ventricle	heart
25	chr21:40766800-40783400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr21:40767000-40777800	Weak transcription	HUVEC	blood vessel
27	chr21:40767200-40777800	Weak transcription	Fetal Kidney	kidney
28	chr21:40767200-40778000	Weak transcription	Left Ventricle	heart
29	chr21:40767200-40778200	Weak transcription	Colon Smooth Muscle	Colon
30	chr21:40767200-40779400	Weak transcription	Hela-S3	cervix
31	chr21:40767200-40781000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr21:40767800-40777200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr21:40767800-40777800	Weak transcription	Brain Hippocampus Middle	brain
34	chr21:40767800-40778000	Weak transcription	Aorta	Aorta
35	chr21:40768000-40777200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr21:40768000-40778000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr21:40768000-40778000	Weak transcription	Fetal Lung	lung
38	chr21:40768000-40779800	Weak transcription	Placenta	Placenta
39	chr21:40768200-40777200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr21:40768200-40777200	Weak transcription	Fetal Intestine Small	intestine
41	chr21:40768200-40777400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr21:40768200-40777800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr21:40768200-40777800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr21:40768200-40781400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr21:40768200-40784600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr21:40768400-40777800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr21:40768800-40777800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr21:40768800-40782200	Weak transcription	Fetal Thymus	thymus
49	chr21:40769000-40779400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr21:40769000-40780000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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