Variant report

Variant	rs2836936
Chromosome Location	chr21:40567352-40567353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40551398..40560769-chr21:40565658..40576445,18	K562	blood:
2	21:40565363-40575691..21:40718004-40719183	GM12878	blood:
3	chr21:40566344..40569096-chr21:40684027..40685984,2	MCF-7	breast:
4	chr21:40566697..40568656-chr21:40592903..40594703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205581	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1013129	0.84[CHD][hapmap]
rs1046289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11700978	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1554933	0.89[JPT][hapmap]
rs1882777	0.84[CHD][hapmap]
rs1888490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2142112	0.82[CHD][hapmap]
rs2178838	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2234545	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2410103	0.88[ASN][1000 genomes]
rs2776311	0.81[CHB][hapmap]
rs2836937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2836963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2836978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2836990	0.89[JPT][hapmap]
rs28397992	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2854727	0.81[CHB][hapmap]
rs28552370	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28665841	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28693867	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28734946	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3761372	0.89[JPT][hapmap]
rs376720	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs379291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs383965	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs420888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs433013	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs446090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs449428	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4816613	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4817994	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4817995	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4817997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4817998	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6517516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6517517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6517522	0.82[CHB][hapmap]
rs7278048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7280764	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7281540	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741795	0.81[CHB][hapmap]
rs8126528	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8129850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8130798	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8132993	0.81[CHB][hapmap]
rs9305665	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs9305669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9305670	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9975728	0.82[AMR][1000 genomes]
rs9975909	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9976346	0.82[AMR][1000 genomes]
rs9977787	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9977926	0.86[EUR][1000 genomes]
rs9979691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap]
rs9979936	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9981595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9984518	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9985148	0.82[AMR][1000 genomes];0.86[EUR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2836936	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs2836936	BRWD1	cis	cerebellum	SCAN
rs2836936	HMGN1	cis	lymphoblastoid	seeQTL
rs2836936	CBR3	cis	cerebellum	SCAN
rs2836936	BRWD1	cis	multi-tissue	Pritchard
rs2836936	CBR1	cis	parietal	SCAN
rs2836936	BRWD1	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr21:40556400-40568400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr21:40556400-40568400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr21:40556400-40568800	Weak transcription	Psoas Muscle	Psoas
14	chr21:40556400-40571000	Weak transcription	Ovary	ovary
15	chr21:40556600-40567400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr21:40556600-40568200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr21:40556600-40568200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr21:40556600-40568200	Weak transcription	Brain Angular Gyrus	brain
19	chr21:40556600-40568200	Weak transcription	Brain Germinal Matrix	brain
20	chr21:40556600-40568200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr21:40556600-40568200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr21:40556600-40568400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr21:40556600-40568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr21:40556600-40568800	Weak transcription	Aorta	Aorta
25	chr21:40556600-40570400	Weak transcription	Colonic Mucosa	Colon
26	chr21:40556600-40571000	Weak transcription	Fetal Stomach	stomach
27	chr21:40556600-40576600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr21:40556800-40567600	Weak transcription	Primary T cells from cord blood	blood
29	chr21:40556800-40567600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr21:40556800-40567600	Weak transcription	Fetal Brain Male	brain
31	chr21:40556800-40567600	Weak transcription	HepG2	liver
32	chr21:40556800-40567800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr21:40556800-40567800	Weak transcription	Fetal Kidney	kidney
34	chr21:40556800-40568200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr21:40556800-40568400	Weak transcription	Fetal Heart	heart
36	chr21:40557000-40567800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr21:40557000-40567800	Weak transcription	Brain Substantia Nigra	brain
38	chr21:40557000-40568600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr21:40557000-40570600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr21:40557200-40567800	Weak transcription	A549	lung
41	chr21:40557200-40569400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr21:40559000-40568600	Weak transcription	Colon Smooth Muscle	Colon
43	chr21:40559200-40568600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr21:40559400-40567600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr21:40560400-40570800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr21:40561000-40567600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr21:40561000-40568200	Weak transcription	HSMMtube	muscle
48	chr21:40562400-40568200	Weak transcription	Thymus	Thymus
49	chr21:40562600-40567800	Weak transcription	HMEC	breast
50	chr21:40562600-40568200	Weak transcription	Right Ventricle	heart

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