Variant report

Variant	rs2836934
Chromosome Location	chr21:40564885-40564886
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40564332..40566016-chr21:40719069..40721056,2	MCF-7	breast:
2	chr21:40564655..40567110-chr21:40569434..40571576,2	MCF-7	breast:
3	chr21:40560024..40562284-chr21:40564214..40567219,3	MCF-7	breast:
4	chr21:40564573..40566805-chr21:40573736..40576146,2	K562	blood:

Variant related genes	Relation type
ENSG00000205581	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1029004	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11088466	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11088470	0.83[EUR][1000 genomes]
rs11700813	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11701805	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11910232	0.86[EUR][1000 genomes]
rs11911087	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12483559	0.85[EUR][1000 genomes]
rs12627205	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13049907	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1980407	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2056844	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2070865	0.92[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs2150411	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2150413	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2150414	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2297256	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836922	0.88[EUR][1000 genomes]
rs2836926	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836930	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836931	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836940	0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836942	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836943	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836945	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836948	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836949	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs2836952	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836956	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836958	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836959	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]
rs2836966	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836980	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2836983	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2836985	0.92[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs3171465	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34705151	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35769610	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35994303	0.81[EUR][1000 genomes]
rs4816617	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4816618	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818001	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818018	0.81[EUR][1000 genomes]
rs4818019	0.82[EUR][1000 genomes]
rs59916147	0.87[EUR][1000 genomes]
rs62223011	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62223039	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7276046	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7278297	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7279497	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7282582	0.88[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs8127379	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8129595	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8130162	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8130240	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8130320	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8131132	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8132143	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8132424	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8133928	0.83[EUR][1000 genomes]
rs8134214	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8134843	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2836934	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs2836934	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2836934	BRWD1	cis	Frontal Cortex	GTEx
rs2836934	PSMG1	cis	Artery Tibial	GTEx
rs2836934	DSCR2	cis	normal skin	skin_eQTL
rs2836934	C21orf107	cis	multi-tissue	Pritchard
rs2836934	BRWD1	cis	Cerebellum	GTEx
rs2836934	BRWD1	cis	Lymphoblastoid	GTEx
rs2836934	BRWD1	cis	Temporal Cortex	GTEx
rs2836934	BRWD1	cis	Brain Pons	GTEx
rs2836934	HMGN1	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40567800	Weak transcription	Left Ventricle	heart
2	chr21:40556200-40568600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr21:40556200-40568800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:40556200-40570200	Weak transcription	Stomach Mucosa	stomach
5	chr21:40556200-40570800	Weak transcription	Small Intestine	intestine
6	chr21:40556200-40571000	Weak transcription	Lung	lung
7	chr21:40556200-40571200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:40556200-40576600	Weak transcription	Esophagus	oesophagus
9	chr21:40556200-40576600	Weak transcription	Pancreas	Pancrea
10	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr21:40556400-40566000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr21:40556400-40568400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr21:40556400-40568400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr21:40556400-40568800	Weak transcription	Psoas Muscle	Psoas
15	chr21:40556400-40571000	Weak transcription	Ovary	ovary
16	chr21:40556600-40565400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr21:40556600-40565800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr21:40556600-40565800	Weak transcription	Fetal Thymus	thymus
19	chr21:40556600-40566000	Weak transcription	Fetal Brain Female	brain
20	chr21:40556600-40566400	Weak transcription	Fetal Muscle Leg	muscle
21	chr21:40556600-40566600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr21:40556600-40566800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr21:40556600-40567400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr21:40556600-40568200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr21:40556600-40568200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr21:40556600-40568200	Weak transcription	Brain Angular Gyrus	brain
27	chr21:40556600-40568200	Weak transcription	Brain Germinal Matrix	brain
28	chr21:40556600-40568200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr21:40556600-40568200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr21:40556600-40568400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr21:40556600-40568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr21:40556600-40568800	Weak transcription	Aorta	Aorta
33	chr21:40556600-40570400	Weak transcription	Colonic Mucosa	Colon
34	chr21:40556600-40571000	Weak transcription	Fetal Stomach	stomach
35	chr21:40556600-40576600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr21:40556800-40565000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr21:40556800-40565400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr21:40556800-40565600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr21:40556800-40566000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr21:40556800-40566000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr21:40556800-40566200	Weak transcription	Primary B cells from cord blood	blood
42	chr21:40556800-40566200	Weak transcription	Brain Anterior Caudate	brain
43	chr21:40556800-40566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr21:40556800-40566400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr21:40556800-40567600	Weak transcription	Primary T cells from cord blood	blood
46	chr21:40556800-40567600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr21:40556800-40567600	Weak transcription	Fetal Brain Male	brain
48	chr21:40556800-40567600	Weak transcription	HepG2	liver
49	chr21:40556800-40567800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr21:40556800-40567800	Weak transcription	Fetal Kidney	kidney

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