Variant report

Variant	rs2836959
Chromosome Location	chr21:40623668-40623669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40555075..40556681-chr21:40622988..40625845,2	K562	blood:
2	chr21:40623160..40626100-chr21:40683274..40685842,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000272991	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1029004	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10854396	0.83[ASN][1000 genomes]
rs11088466	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11088470	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11701805	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11702505	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11910232	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11911087	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11911822	0.96[YRI][hapmap]
rs12483559	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12626405	0.83[AFR][1000 genomes]
rs12627205	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13047518	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13049907	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13051519	0.81[EUR][1000 genomes]
rs1571709	0.86[YRI][hapmap]
rs1980407	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2056844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2070865	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2150411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2150413	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2150414	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2183573	0.93[ASW][hapmap];0.96[YRI][hapmap]
rs2297256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836926	0.96[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2836930	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836931	0.96[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836934	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2836940	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836945	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836949	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836952	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836966	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836969	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs2836971	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs2836975	0.93[ASW][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2836980	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836983	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836984	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836985	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3171465	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34705151	0.86[EUR][1000 genomes]
rs35769610	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35994303	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs377098	0.96[YRI][hapmap]
rs418298	0.93[ASW][hapmap];0.96[YRI][hapmap]
rs418359	0.93[ASW][hapmap];0.96[YRI][hapmap]
rs419469	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs4816617	0.87[EUR][1000 genomes]
rs4816618	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4818015	0.93[ASW][hapmap];0.96[YRI][hapmap]
rs4818018	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4818019	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59916147	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62223011	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62223039	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62223052	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6517522	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs6517535	0.80[AFR][1000 genomes]
rs7276046	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7276774	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs7278297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279497	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs7282582	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes]
rs7282604	0.93[ASW][hapmap];0.96[YRI][hapmap]
rs8127379	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8128191	0.86[YRI][hapmap]
rs8129595	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8130162	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8130240	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8130320	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8131132	0.87[EUR][1000 genomes]
rs8132143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8132295	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs8132333	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs8132424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8133928	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8134214	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8134843	0.87[EUR][1000 genomes]
rs9974757	0.84[AFR][1000 genomes]
rs9982111	0.83[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	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv587481	chr21:40598721-40627020	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2836959	BRWD1	cis	cerebellum	SCAN
rs2836959	BRWD1	cis	Temporal Cortex	GTEx
rs2836959	HMGN1	cis	multi-tissue	Pritchard
rs2836959	C21orf107	cis	multi-tissue	Pritchard
rs2836959	BRWD1	cis	Cerebellum	GTEx
rs2836959	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2836959	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2836959	BRWD1	cis	Brain Pons	GTEx
rs2836959	PSMG1	cis	parietal	SCAN
rs2836959	PSMG1	cis	Artery Tibial	GTEx
rs2836959	BRWD1	cis	Lymphoblastoid	GTEx
rs2836959	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs2836959	BRWD1	cis	Frontal Cortex	GTEx
rs2836959	HMGN1	cis	lymphoblastoid	seeQTL
rs2836959	BRWD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
2	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr21:40565400-40653600	Strong transcription	Dnd41	blood
9	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
11	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
12	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr21:40591400-40625200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr21:40593400-40650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr21:40595800-40624000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr21:40597200-40635600	Weak transcription	Fetal Heart	heart
18	chr21:40598200-40629800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr21:40598600-40625000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr21:40599200-40623800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr21:40603000-40627800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr21:40603200-40653400	Weak transcription	Right Atrium	heart
23	chr21:40608400-40628400	Weak transcription	Lung	lung
24	chr21:40608400-40632200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr21:40608400-40632600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr21:40608400-40634200	Weak transcription	NHLF	lung
27	chr21:40608400-40638200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr21:40608600-40627000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr21:40608600-40628400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr21:40608600-40636400	Weak transcription	Aorta	Aorta
32	chr21:40608800-40627200	Weak transcription	Esophagus	oesophagus
33	chr21:40609200-40627600	Weak transcription	Right Ventricle	heart
34	chr21:40609800-40635400	Weak transcription	Fetal Brain Male	brain
35	chr21:40610800-40626400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr21:40612200-40628600	Weak transcription	Brain Anterior Caudate	brain
37	chr21:40613400-40652000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr21:40613800-40651000	Strong transcription	Fetal Thymus	thymus
39	chr21:40614000-40654400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr21:40614200-40628400	Strong transcription	Fetal Intestine Large	intestine
41	chr21:40614600-40624200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr21:40614600-40654200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr21:40614800-40635000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr21:40614800-40652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr21:40615800-40639800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr21:40616400-40630600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr21:40616400-40631000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr21:40616400-40651800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr21:40616600-40631400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr21:40617200-40628400	Weak transcription	Pancreas	Pancrea

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