Variant report

Variant	rs2836920
Chromosome Location	chr21:40512918-40512919
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	chr21:40510400..40513231-chr21:40543970..40546518,2	K562	blood:

Variant related genes	Relation type
ENSG00000235701	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1078306	1.00[CHB][hapmap]
rs11911112	0.80[ASN][1000 genomes]
rs11911149	0.80[ASN][1000 genomes]
rs12481860	0.80[ASN][1000 genomes]
rs12482156	0.87[ASN][1000 genomes]
rs12482181	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs12482857	0.87[ASN][1000 genomes]
rs12483216	0.80[ASN][1000 genomes]
rs13047550	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13049280	1.00[JPT][hapmap];0.85[YRI][hapmap]
rs13339986	0.81[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13625	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs14194	0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs1541102	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs1571709	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1984022	0.82[CEU][hapmap]
rs2026265	0.84[CEU][hapmap]
rs2026267	1.00[JPT][hapmap]
rs2150415	0.83[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap]
rs2234543	0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs2836901	1.00[CHB][hapmap]
rs2836915	1.00[CHB][hapmap]
rs2836917	1.00[CHB][hapmap]
rs2836921	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2836923	0.83[ASN][1000 genomes]
rs2836924	0.80[ASN][1000 genomes]
rs2836925	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs2836927	0.80[ASN][1000 genomes]
rs2836928	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2836929	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs2836932	0.80[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs2836933	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2836939	1.00[YRI][hapmap]
rs2836955	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2836957	0.82[JPT][hapmap]
rs2836964	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs2836965	0.80[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs2836967	1.00[JPT][hapmap]
rs2836968	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs2836974	0.80[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs34176878	0.80[ASN][1000 genomes]
rs34394827	0.80[ASN][1000 genomes]
rs34478864	0.80[ASN][1000 genomes]
rs34592564	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35386515	0.80[ASN][1000 genomes]
rs35391055	0.80[ASN][1000 genomes]
rs3945	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4817996	0.80[ASN][1000 genomes]
rs6517513	0.80[ASN][1000 genomes]
rs6517514	0.80[ASN][1000 genomes]
rs6517519	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs6517521	0.80[ASN][1000 genomes]
rs6517523	0.80[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs6517526	0.80[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs6517538	0.80[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs68090597	0.80[ASN][1000 genomes]
rs71184665	0.80[ASN][1000 genomes]
rs7280375	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs7283516	1.00[JPT][hapmap]
rs73221193	0.80[ASN][1000 genomes]
rs8127087	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8128026	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8128102	0.84[CEU][hapmap]
rs8128191	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8130556	0.87[ASN][1000 genomes]
rs8130984	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs8132285	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs8132295	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs8132333	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs8132419	0.80[ASN][1000 genomes]
rs8132568	0.80[ASN][1000 genomes]
rs9941894	0.80[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]

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	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
3	esv3395554	chr21:40512728-40517052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2836920	PSMG1	cis	lymphoblastoid	seeQTL
rs2836920	BRWD1	cis	cerebellum	SCAN
rs2836920	DSCR2	cis	normal skin	skin_eQTL
rs2836920	BRWD1	cis	parietal	SCAN
rs2836920	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2836920	PIGP	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40509400-40513600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr21:40509600-40513200	Weak transcription	Placenta	Placenta
3	chr21:40509800-40513200	Weak transcription	Fetal Muscle Leg	muscle
4	chr21:40509800-40513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:40509800-40513800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr21:40509800-40515800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr21:40510200-40513400	Weak transcription	Fetal Lung	lung
8	chr21:40510600-40515000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr21:40511600-40513400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr21:40512000-40514200	Enhancers	Fetal Thymus	thymus
11	chr21:40512400-40513000	Weak transcription	Thymus	Thymus
12	chr21:40512800-40514200	Enhancers	Sigmoid Colon	Sigmoid Colon

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