Variant report

Variant	rs2836996
Chromosome Location	chr21:40750439-40750440
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40683876..40687631-chr21:40749667..40753921,6	K562	blood:
2	chr21:40681416..40687854-chr21:40744378..40751195,8	K562	blood:
3	chr21:40748679..40750814-chr21:40758912..40761248,3	K562	blood:
4	21:40686083-40686932..21:40748850-40752541	K562	blood:
5	chr21:40552640..40555791-chr21:40749339..40752310,3	K562	blood:
6	chr21:40719359..40724848-chr21:40748806..40754741,7	MCF-7	breast:
7	chr21:40749644..40752104-chr21:40816911..40820267,3	MCF-7	breast:
8	21:40712819-40717370..21:40748850-40752541	GM12878	blood:
9	chr21:40748679..40750675-chr21:40758576..40761248,3	K562	blood:
10	chr21:40716662..40723444-chr21:40748337..40754328,16	MCF-7	breast:
11	chr21:40744313..40747019-chr21:40749463..40751747,2	K562	blood:
12	chr21:40750392..40754801-chr21:40757428..40762186,12	MCF-7	breast:
13	21:40718004-40719183..21:40748850-40752541	GM12878	blood:
14	chr21:40719750..40724652-chr21:40748317..40754270,9	K562	blood:
15	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
16	chr21:40690460..40692960-chr21:40749748..40751781,2	K562	blood:
17	21:40348344-40365490..21:40748850-40752541	Hela-S3	cervix:
18	chr21:40683717..40685708-chr21:40747929..40750593,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232837	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000205581	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1060180	0.93[CHB][hapmap]
rs10775662	0.93[CHB][hapmap]
rs1554933	0.88[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2063999	0.84[CHB][hapmap]
rs2244352	0.89[YRI][hapmap]
rs2836990	0.92[YRI][hapmap]
rs2836994	0.92[CHB][hapmap]
rs2836995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836997	1.00[CHB][hapmap]
rs2836998	0.93[CHB][hapmap]
rs2836999	0.92[CHB][hapmap]
rs2837002	0.92[CHB][hapmap]
rs2837003	0.92[CHB][hapmap];1.00[YRI][hapmap]
rs2837004	0.92[CHB][hapmap];1.00[YRI][hapmap]
rs2837005	0.92[CHB][hapmap]
rs2837006	0.92[CHB][hapmap]
rs2837007	0.92[CHB][hapmap]
rs2837008	0.92[CHB][hapmap]
rs28550626	0.81[AFR][1000 genomes]
rs3761372	0.88[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs4816624	0.85[CHB][hapmap]
rs4818034	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6517547	0.93[CHB][hapmap]
rs8132324	0.81[AFR][1000 genomes]
rs9974263	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9974828	0.92[CHB][hapmap]
rs9975761	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9983270	0.81[AFR][1000 genomes]
rs9983594	0.81[AFR][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	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2836996	LCA5L	cis	lung	GTEx
rs2836996	LCA5L	cis	Thyroid	GTEx
rs2836996	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2836996	WRB	cis	Nerve Tibial	GTEx
rs2836996	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2836996	WRB	cis	Thyroid	GTEx
rs2836996	WRB	cis	lung	GTEx
rs2836996	LCA5L	cis	Nerve Tibial	GTEx
rs2836996	WRB	cis	Adipose Subcutaneous	GTEx
rs2836996	WRB	cis	Whole Blood	GTEx
rs2836996	WRB	cis	Esophagus Muscularis	GTEx
rs2836996	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2836996	LCA5L	cis	Esophagus Muscularis	GTEx
rs2836996	LCA5L	cis	Whole Blood	GTEx
rs2836996	LCA5L	cis	Artery Tibial	GTEx
rs2836996	WRB	cis	Artery Tibial	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40743000-40751600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr21:40745800-40751400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr21:40746000-40751600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr21:40746000-40751600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr21:40746200-40751600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40746200-40751600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:40746200-40751600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr21:40746200-40751600	Weak transcription	Brain Anterior Caudate	brain
9	chr21:40746200-40751600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr21:40746200-40751600	Weak transcription	GM12878-XiMat	blood
11	chr21:40746200-40751800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr21:40746200-40751800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr21:40746200-40752000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr21:40746400-40751600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr21:40747000-40751600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr21:40747200-40751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr21:40749400-40751600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr21:40749600-40751600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr21:40749600-40751600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr21:40749600-40751600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr21:40749600-40751600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr21:40749600-40751800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr21:40749600-40752200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr21:40749800-40751600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr21:40749800-40751600	Weak transcription	Stomach Mucosa	stomach
26	chr21:40749800-40751600	Weak transcription	HepG2	liver
27	chr21:40749800-40751600	Weak transcription	HMEC	breast
28	chr21:40749800-40751600	Weak transcription	NHEK	skin
29	chr21:40749800-40751800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr21:40749800-40752000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr21:40750000-40751600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr21:40750400-40751600	Weak transcription	Hela-S3	cervix
33	chr21:40750400-40751600	Weak transcription	K562	blood

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