Variant report

Variant	rs2836930
Chromosome Location	chr21:40545656-40545657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40545350-40545861	HL-60	blood:	n/a	n/a
2	POLR2A	chr21:40545470-40545736	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr21:40545407-40546233	HepG2	liver:	n/a	n/a
4	POLR2A	chr21:40545411-40545988	GM12878	blood:	n/a	n/a
5	POLR2A	chr21:40540854-40546714	HepG2	liver:	n/a	n/a
6	POLR2A	chr21:40545394-40546036	K562	blood:	n/a	n/a
7	POLR2A	chr21:40539073-40546427	K562	blood:	n/a	n/a
8	POLR2A	chr21:40545446-40545895	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr21:40545373-40545679	K562	blood:	n/a	n/a
10	POLR2A	chr21:40545440-40545814	GM12891	blood:	n/a	n/a
11	POLR2A	chr21:40545492-40545702	GM12878	blood:	n/a	n/a
12	POLR2A	chr21:40545361-40545718	GM12891	blood:	n/a	n/a
13	POLR2A	chr21:40545310-40546272	K562	blood:	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
ENSG00000235701	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000272991	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1029004	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11088466	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11088470	0.85[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	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11702505	0.81[AMR][1000 genomes]
rs11910232	0.85[EUR][1000 genomes]
rs11911087	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11911822	1.00[YRI][hapmap]
rs12483559	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12627205	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13049907	0.83[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];0.80[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2070865	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs2150411	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2150413	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2150414	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2183573	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs2297256	0.96[CEU][hapmap];0.95[JPT][hapmap];0.91[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];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836931	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];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836940	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836942	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836943	1.00[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836945	1.00[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836948	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.86[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];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836956	0.96[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836958	0.96[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836959	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836966	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[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];0.85[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836983	0.93[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836984	0.81[AMR][1000 genomes]
rs2836985	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs3171465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34705151	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35769610	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs371625	0.81[AFR][1000 genomes]
rs377098	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs414850	0.81[AFR][1000 genomes]
rs418298	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs418359	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs419469	1.00[YRI][hapmap]
rs429955	0.81[AFR][1000 genomes]
rs442972	0.81[AFR][1000 genomes]
rs452377	0.81[AFR][1000 genomes]
rs4816617	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816618	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4817999	0.83[AFR][1000 genomes]
rs4818001	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4818015	1.00[YRI][hapmap]
rs4818018	0.85[AMR][1000 genomes]
rs4818019	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59916147	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62223011	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62223039	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62223052	0.83[AMR][1000 genomes]
rs6517518	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs6517522	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs7276046	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7276774	0.96[YRI][hapmap]
rs7278297	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7279497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282582	0.88[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs7282604	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs8127379	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8128191	0.90[YRI][hapmap]
rs8129595	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8130162	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8130240	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130320	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8131132	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132143	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8132295	0.90[YRI][hapmap]
rs8132333	0.90[YRI][hapmap]
rs8132424	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8133928	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8134214	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8134843	0.87[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
rs2836930	BRWD1	cis	Frontal Cortex	GTEx
rs2836930	C21orf107	cis	multi-tissue	Pritchard
rs2836930	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs2836930	HMGN1	cis	multi-tissue	Pritchard
rs2836930	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2836930	BRWD1	cis	Lymphoblastoid	GTEx
rs2836930	PSMG1	cis	Artery Tibial	GTEx
rs2836930	BRWD1	cis	Temporal Cortex	GTEx
rs2836930	BRWD1	cis	Cerebellum	GTEx
rs2836930	BRWD1	cis	Brain Pons	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	chr21:40541200-40546400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr21:40541200-40546400	Strong transcription	Adipose Nuclei	Adipose
11	chr21:40541200-40546400	Strong transcription	Fetal Muscle Leg	muscle
12	chr21:40541200-40546600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr21:40541200-40546600	Strong transcription	Thymus	Thymus
14	chr21:40541200-40547800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr21:40541200-40548400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr21:40541200-40550600	Strong transcription	Dnd41	blood
17	chr21:40541200-40552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr21:40541200-40552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr21:40541200-40553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr21:40541200-40553000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
24	chr21:40541400-40545800	Weak transcription	Brain Angular Gyrus	brain
25	chr21:40541400-40546400	Strong transcription	Fetal Stomach	stomach
26	chr21:40541400-40546800	Strong transcription	A549	lung
27	chr21:40541400-40553000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr21:40541600-40545800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr21:40541600-40553800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr21:40541600-40554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr21:40541600-40554000	Weak transcription	Colon Smooth Muscle	Colon
33	chr21:40541800-40545800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr21:40541800-40545800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
36	chr21:40542000-40554000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr21:40542000-40554000	Weak transcription	Stomach Mucosa	stomach
38	chr21:40542200-40551600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr21:40542400-40548600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
41	chr21:40542800-40545800	Strong transcription	K562	blood
42	chr21:40542800-40546400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr21:40542800-40546400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr21:40542800-40546800	Strong transcription	Placenta	Placenta
45	chr21:40542800-40547400	Weak transcription	Fetal Heart	heart
46	chr21:40542800-40554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr21:40543000-40546400	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr21:40543000-40546400	Strong transcription	Ovary	ovary
49	chr21:40543000-40546600	Strong transcription	Liver	Liver
50	chr21:40543000-40546600	Strong transcription	Fetal Thymus	thymus

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