Variant report

Variant	rs2410123
Chromosome Location	chr21:40700093-40700094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40696801..40699302-chr21:40699637..40702550,2	K562	blood:
2	chr21:40699788..40702624-chr21:40715350..40718145,2	K562	blood:
3	chr21:40696329..40702419-chr21:40706472..40712889,11	K562	blood:
4	21:40695608-40702099..21:40757151-40764378	K562	blood:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000252915	Chromatin interaction

Extended variants
information (count: 146 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1011413	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10154217	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1041439	0.84[CHB][hapmap]
rs11088471	0.95[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11088472	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11910705	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11910906	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11910971	0.84[CHB][hapmap]
rs11911822	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12482181	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs12626405	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13051430	0.84[CHB][hapmap]
rs13625	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs14194	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs1541100	0.84[CHB][hapmap]
rs1541102	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs1882779	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1888487	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1888488	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963676	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1984022	0.96[YRI][hapmap]
rs1984748	0.84[CHB][hapmap]
rs2005933	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026265	0.96[YRI][hapmap]
rs2026266	0.84[CHB][hapmap]
rs2026267	0.83[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap]
rs2037925	1.00[ASW][hapmap];0.96[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];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2142111	0.92[CEU][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs2142117	0.84[CHB][hapmap]
rs2150410	0.84[CHB][hapmap]
rs2150413	0.92[ASW][hapmap];0.85[YRI][hapmap]
rs2150414	0.92[ASW][hapmap];0.85[YRI][hapmap]
rs2150415	0.92[ASW][hapmap];0.95[YRI][hapmap]
rs2183573	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs2183575	0.83[CHB][hapmap]
rs2183576	0.83[CHB][hapmap]
rs2234543	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2245455	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs2272576	0.95[CHB][hapmap]
rs2272577	0.95[CHB][hapmap]
rs2410104	0.84[CHB][hapmap]
rs2410124	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2735306	0.88[MEX][hapmap]
rs2776307	0.83[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap]
rs2776309	0.83[LWK][hapmap]
rs2836925	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836929	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836932	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836933	0.96[YRI][hapmap]
rs2836956	0.92[ASW][hapmap];0.85[YRI][hapmap]
rs2836957	0.96[YRI][hapmap]
rs2836958	0.92[ASW][hapmap];0.85[YRI][hapmap]
rs2836964	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836965	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836967	0.96[YRI][hapmap]
rs2836968	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836969	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2836971	0.88[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2836974	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836975	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2836981	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836982	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836985	0.92[ASW][hapmap];0.82[YRI][hapmap]
rs2836986	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836987	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836988	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];0.98[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34240248	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34436313	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35182074	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35909862	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs371625	0.83[AMR][1000 genomes]
rs377098	0.92[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes]
rs414850	0.80[AMR][1000 genomes]
rs418298	0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes]
rs418359	0.92[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes]
rs419469	0.85[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs428602	0.92[CEU][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs429955	0.80[AMR][1000 genomes]
rs442972	0.83[AMR][1000 genomes]
rs452377	0.83[AMR][1000 genomes]
rs4624474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4816619	0.84[CHB][hapmap]
rs4816620	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4816623	0.82[ASN][1000 genomes]
rs4817999	0.80[AMR][1000 genomes]
rs4818005	0.89[AMR][1000 genomes]
rs4818007	0.84[CHB][hapmap]
rs4818011	0.84[CHB][hapmap]
rs4818015	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818017	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61300849	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6517519	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs6517523	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs6517526	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs6517529	0.84[CHB][hapmap]
rs6517531	0.83[CHB][hapmap]
rs6517532	0.84[CHB][hapmap]
rs6517535	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6517538	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs6517541	0.95[CHB][hapmap]
rs718225	0.84[CHB][hapmap]
rs719230	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7275773	0.84[CHB][hapmap]
rs7276774	0.87[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7277978	0.90[AFR][1000 genomes]
rs7278297	0.85[YRI][hapmap]
rs7278985	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7279558	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7280326	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7280375	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs7281853	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7282604	0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes]
rs7283439	0.84[CHB][hapmap]
rs7283516	0.96[YRI][hapmap]
rs8127087	0.96[YRI][hapmap]
rs8127391	0.84[CHB][hapmap]
rs8127986	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8128026	0.95[YRI][hapmap]
rs8128102	0.92[YRI][hapmap]
rs8128118	0.86[CHB][hapmap]
rs8130795	0.83[AMR][1000 genomes]
rs8130854	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8130984	0.96[YRI][hapmap]
rs8131150	0.84[CHB][hapmap]
rs8131263	0.84[CHB][hapmap]
rs8132230	0.84[CHB][hapmap]
rs8132285	0.96[YRI][hapmap]
rs9636957	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs973521	0.84[CHB][hapmap]
rs997147	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9974757	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9975119	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9975562	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9975614	0.84[ASN][1000 genomes]
rs9978591	0.84[CHB][hapmap]
rs9978775	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9979483	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9981301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9981656	0.82[ASN][1000 genomes]
rs9982111	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
4	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
5	nsv587482	chr21:40684427-40706594	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2410123	PSMG1	cis	lung	GTEx
rs2410123	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2410123	LOC643790	trans	multi-tissue	Pritchard
rs2410123	BRWD1	cis	lymphoblastoid	seeQTL
rs2410123	PSMG1	cis	Artery Tibial	GTEx
rs2410123	BRWD1	cis	Lymphoblastoid	GTEx
rs2410123	BRWD1	cis	Frontal Cortex	GTEx
rs2410123	PSMG1	cis	parietal	SCAN
rs2410123	PSMG1	cis	lymphoblastoid	seeQTL
rs2410123	PSMG1	cis	Esophagus Mucosa	GTEx
rs2410123	C21orf107	cis	multi-tissue	Pritchard
rs2410123	BRWD1	cis	parietal	SCAN
rs2410123	BRWD1	cis	Temporal Cortex	GTEx
rs2410123	BRWD1	cis	cerebellum	SCAN
rs2410123	HMGN1	cis	multi-tissue	Pritchard
rs2410123	BRWD1	cis	Brain Pons	GTEx
rs2410123	BRWD1	cis	Cerebellum	GTEx
rs2410123	DSCR2	cis	multi-tissue	Pritchard
rs2410123	BRWD1	cis	multi-tissue	Pritchard
rs2410123	DSCR2	cis	normal skin	skin_eQTL
rs2410123	DSCR2	cis	lesional skin	skin_eQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40692400-40718400	Weak transcription	Right Atrium	heart
2	chr21:40699200-40704200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40699200-40712600	Weak transcription	Fetal Muscle Leg	muscle
4	chr21:40699400-40703800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr21:40699400-40703800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr21:40699400-40703800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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