Variant report

Variant	rs2836931
Chromosome Location	chr21:40546569-40546570
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40540854-40546714	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40495398..40498019-chr21:40544324..40546654,2	K562	blood:
2	chr21:40174974..40176584-chr21:40544801..40546577,2	K562	blood:
3	chr21:40544095..40546729-chr21:40827156..40828956,2	K562	blood:
4	chr21:40542935..40544954-chr21:40544958..40548517,4	MCF-7	breast:
5	chr21:40529860..40532688-chr21:40545443..40547905,2	K562	blood:
6	chr21:40544824..40547305-chr21:40554591..40556677,3	MCF-7	breast:

No data

Variant related genes	Relation type
PCBP2P1	TF binding region
ENSG00000272991	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000235701	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1029004	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11088466	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11088470	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11700813	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701805	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11910232	0.85[EUR][1000 genomes]
rs11911087	0.84[EUR][1000 genomes]
rs11911822	1.00[YRI][hapmap]
rs12483559	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12627205	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13049907	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1571709	0.90[YRI][hapmap]
rs1980407	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037923	0.82[ASN][1000 genomes]
rs2056844	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs2070865	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs2150411	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2150413	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2150414	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2183573	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs2297256	0.96[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836922	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836934	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836940	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836942	0.96[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836943	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836945	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836948	0.96[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836949	0.96[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs2836952	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836956	0.96[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836958	0.96[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836959	0.96[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836966	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836969	1.00[YRI][hapmap]
rs2836971	1.00[YRI][hapmap]
rs2836975	1.00[YRI][hapmap]
rs2836980	0.92[CEU][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836983	0.92[CEU][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836985	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs3171465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34705151	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35769610	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs377098	1.00[YRI][hapmap]
rs418298	1.00[YRI][hapmap]
rs418359	1.00[YRI][hapmap]
rs419469	1.00[YRI][hapmap]
rs4816617	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816618	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4817999	0.83[AFR][1000 genomes]
rs4818001	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4818015	1.00[YRI][hapmap]
rs4818018	0.83[AMR][1000 genomes]
rs4818019	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59916147	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62223011	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62223039	0.83[EUR][1000 genomes]
rs62223052	0.81[AMR][1000 genomes]
rs6517518	0.87[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6517522	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs7276046	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7276774	0.96[YRI][hapmap]
rs7278297	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7279497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282582	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs7282604	1.00[YRI][hapmap]
rs8127379	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8128191	0.90[YRI][hapmap]
rs8129595	0.81[EUR][1000 genomes]
rs8130162	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8130240	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130320	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8131132	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132143	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8132295	0.89[YRI][hapmap]
rs8132333	0.89[YRI][hapmap]
rs8132424	0.96[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8133928	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8134214	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8134843	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2836931	BRWD1	cis	Lymphoblastoid	GTEx
rs2836931	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2836931	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs2836931	BRWD1	cis	Temporal Cortex	GTEx
rs2836931	HMGN1	cis	multi-tissue	Pritchard
rs2836931	BRWD1	cis	Frontal Cortex	GTEx
rs2836931	BRWD1	cis	Brain Pons	GTEx
rs2836931	PSMG1	cis	Artery Tibial	GTEx
rs2836931	C21orf107	cis	multi-tissue	Pritchard
rs2836931	BRWD1	cis	Cerebellum	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40537600-40553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:40538800-40550400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr21:40539000-40550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
7	chr21:40541000-40547000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr21:40541000-40547600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr21:40541200-40546600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr21:40541200-40546600	Strong transcription	Thymus	Thymus
11	chr21:40541200-40547800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr21:40541200-40548400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr21:40541200-40550600	Strong transcription	Dnd41	blood
14	chr21:40541200-40552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr21:40541200-40552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr21:40541200-40553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr21:40541200-40553000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
21	chr21:40541400-40546800	Strong transcription	A549	lung
22	chr21:40541400-40553000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr21:40541600-40553800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr21:40541600-40554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr21:40541600-40554000	Weak transcription	Colon Smooth Muscle	Colon
27	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
28	chr21:40542000-40554000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr21:40542000-40554000	Weak transcription	Stomach Mucosa	stomach
30	chr21:40542200-40551600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr21:40542400-40548600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
33	chr21:40542800-40546800	Strong transcription	Placenta	Placenta
34	chr21:40542800-40547400	Weak transcription	Fetal Heart	heart
35	chr21:40542800-40554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr21:40543000-40546600	Strong transcription	Liver	Liver
37	chr21:40543000-40546600	Strong transcription	Fetal Thymus	thymus
38	chr21:40543000-40546600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr21:40543000-40546600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr21:40543000-40546800	Strong transcription	Primary T cells from cord blood	blood
41	chr21:40543000-40547000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr21:40543000-40547600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr21:40543000-40547800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr21:40543000-40548000	Strong transcription	Fetal Intestine Small	intestine
45	chr21:40543000-40549400	Strong transcription	HepG2	liver
46	chr21:40543000-40552400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr21:40543000-40552400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr21:40543000-40552600	Strong transcription	Osteobl	bone
49	chr21:40543200-40548200	Strong transcription	NH-A	brain
50	chr21:40543200-40549000	Strong transcription	Rectal Mucosa Donor 29	rectum

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