Variant report

Variant	rs9979936
Chromosome Location	chr21:40652389-40652390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40652010-40653498	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40651445..40653004-chr21:40721446..40723113,2	MCF-7	breast:
2	chr21:40650313..40652723-chr21:40719146..40721312,2	MCF-7	breast:
3	chr21:40652004..40654564-chr21:40716456..40719134,2	MCF-7	breast:

Variant related genes	Relation type
BRWD1	TF binding region
ENSG00000252915	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000205581	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1046289	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11700978	0.84[EUR][1000 genomes]
rs12329720	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12329767	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2178838	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234545	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2297255	0.86[EUR][1000 genomes]
rs2836936	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836937	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836941	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836946	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836947	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836962	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836963	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836970	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836976	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836978	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836979	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397992	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28460573	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28494168	0.81[EUR][1000 genomes]
rs28542479	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28552370	0.86[EUR][1000 genomes]
rs28580194	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28590100	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28665841	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28684434	0.81[EUR][1000 genomes]
rs28693867	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734946	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs376720	0.84[EUR][1000 genomes]
rs379291	0.86[EUR][1000 genomes]
rs383965	0.81[EUR][1000 genomes]
rs420888	0.86[EUR][1000 genomes]
rs433013	0.84[EUR][1000 genomes]
rs446090	0.86[EUR][1000 genomes]
rs449428	0.84[EUR][1000 genomes]
rs4817998	0.84[EUR][1000 genomes]
rs6517516	0.84[EUR][1000 genomes]
rs6517517	0.84[EUR][1000 genomes]
rs7278048	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7281540	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8129850	0.86[EUR][1000 genomes]
rs8130798	0.86[EUR][1000 genomes]
rs9305669	0.86[EUR][1000 genomes]
rs9305670	0.86[EUR][1000 genomes]
rs997146	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9975256	0.81[EUR][1000 genomes]
rs9975728	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975909	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9975937	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9976346	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977787	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9977926	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979691	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9981349	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9981595	0.86[EUR][1000 genomes]
rs9982825	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9984518	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9984922	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9985067	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9985148	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9979936	BRWD1	cis	multi-tissue	Pritchard
rs9979936	BRWD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr21:40565400-40653600	Strong transcription	Dnd41	blood
7	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr21:40603200-40653400	Weak transcription	Right Atrium	heart
10	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr21:40614000-40654400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr21:40614600-40654200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr21:40614800-40652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:40618000-40659200	Weak transcription	Stomach Mucosa	stomach
15	chr21:40619400-40656200	Weak transcription	Ovary	ovary
16	chr21:40619600-40660200	Weak transcription	Brain Angular Gyrus	brain
17	chr21:40625800-40652400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr21:40626200-40653400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr21:40626800-40654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr21:40630200-40661600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr21:40630200-40662800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr21:40630400-40653800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr21:40631200-40663600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr21:40631600-40653400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr21:40631800-40653600	Strong transcription	Fetal Intestine Large	intestine
26	chr21:40633200-40653600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr21:40633200-40662800	Weak transcription	Esophagus	oesophagus
28	chr21:40635800-40653400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr21:40635800-40653600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr21:40636600-40659000	Weak transcription	Colon Smooth Muscle	Colon
31	chr21:40638200-40665000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr21:40638600-40657000	Weak transcription	HMEC	breast
33	chr21:40638600-40659800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:40638600-40663400	Weak transcription	Gastric	stomach
35	chr21:40638600-40663400	Weak transcription	Psoas Muscle	Psoas
36	chr21:40638600-40665600	Weak transcription	Spleen	Spleen
37	chr21:40639000-40659200	Weak transcription	Brain Substantia Nigra	brain
38	chr21:40639000-40662600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr21:40639000-40663400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr21:40639200-40659600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr21:40641000-40661400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
43	chr21:40642600-40652400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr21:40642600-40653600	Strong transcription	Liver	Liver
45	chr21:40642600-40658800	Weak transcription	A549	lung
46	chr21:40642600-40659200	Weak transcription	HUVEC	blood vessel
47	chr21:40643000-40662800	Weak transcription	NHLF	lung
48	chr21:40643400-40662800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr21:40643400-40662800	Weak transcription	Brain Hippocampus Middle	brain
50	chr21:40643600-40663600	Weak transcription	Brain Cingulate Gyrus	brain

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