Variant report

Variant	rs9941894
Chromosome Location	chr21:40634058-40634059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40629267..40631101-chr21:40633263..40636157,2	K562	blood:
2	chr21:40633679..40635418-chr21:40692095..40693718,2	MCF-7	breast:
3	chr21:40631221..40636644-chr21:40641722..40645540,5	MCF-7	breast:
4	chr21:40631854..40634672-chr21:40643300..40644841,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1041440	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427502	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1065242	0.84[EUR][1000 genomes]
rs11910151	0.83[EUR][1000 genomes]
rs12151994	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12481860	0.81[EUR][1000 genomes]
rs12482181	0.96[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs12483216	0.81[EUR][1000 genomes]
rs12710453	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710454	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13047663	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13047678	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13048178	0.84[EUR][1000 genomes]
rs13049280	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13052882	0.81[EUR][1000 genomes]
rs13339986	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13625	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs14194	0.87[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs1541102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571709	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1984022	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2026265	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2026267	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs2150415	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2234543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs2249651	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2735306	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs2776307	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs2776309	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs28360661	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836920	0.80[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs2836925	0.96[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs2836927	0.81[EUR][1000 genomes]
rs2836928	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836929	0.96[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs2836932	0.92[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs2836933	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2836938	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836939	0.81[MEX][hapmap];1.00[YRI][hapmap]
rs2836944	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836953	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2836955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836964	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836968	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836972	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836973	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836977	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2989330	0.89[AMR][1000 genomes]
rs34035316	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34176878	0.82[EUR][1000 genomes]
rs34294410	0.81[EUR][1000 genomes]
rs34433511	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34578707	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672724	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34978594	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35064900	0.81[EUR][1000 genomes]
rs35068861	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35386515	0.81[EUR][1000 genomes]
rs35560196	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571600	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36113648	0.81[EUR][1000 genomes]
rs3945	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55740356	0.83[AMR][1000 genomes]
rs55836299	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56306759	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6517519	0.96[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs6517521	0.82[EUR][1000 genomes]
rs6517523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs6517526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517527	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517533	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66465538	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004583	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68090597	0.81[EUR][1000 genomes]
rs7277978	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7280375	0.96[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7282624	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283420	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283569	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73221193	0.83[EUR][1000 genomes]
rs7354783	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127087	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs8128026	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs8128102	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128191	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs8128620	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128734	0.84[EUR][1000 genomes]
rs8128894	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129147	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8129355	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129416	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8130984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132285	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8132295	0.96[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs8132333	0.96[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs8133146	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8134733	0.84[AMR][1000 genomes];0.92[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs9941894	PSMG1	cis	Esophagus Mucosa	GTEx
rs9941894	PSMG1	cis	Artery Tibial	GTEx
rs9941894	DSCR2	cis	normal skin	skin_eQTL
rs9941894	HMGN1	cis	multi-tissue	Pritchard
rs9941894	BRWD1	cis	multi-tissue	Pritchard
rs9941894	BRWD1	cis	parietal	SCAN
rs9941894	PSMG1	cis	parietal	SCAN
rs9941894	BRWD1	cis	cerebellum	SCAN
rs9941894	DSCR2	cis	uninvolved skin	skin_eQTL
rs9941894	PIGP	cis	parietal	SCAN
rs9941894	CLIC6	cis	parietal	SCAN
rs9941894	DSCR2	cis	multi-tissue	Pritchard
rs9941894	PSMG1	cis	lung	GTEx
rs9941894	LOC643790	trans	multi-tissue	Pritchard
rs9941894	DSCR3	cis	cerebellum	SCAN
rs9941894	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs9941894	PSMG1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
2	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr21:40565400-40653600	Strong transcription	Dnd41	blood
9	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
11	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr21:40593400-40650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr21:40597200-40635600	Weak transcription	Fetal Heart	heart
15	chr21:40603200-40653400	Weak transcription	Right Atrium	heart
16	chr21:40608400-40634200	Weak transcription	NHLF	lung
17	chr21:40608400-40638200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr21:40608600-40636400	Weak transcription	Aorta	Aorta
20	chr21:40609800-40635400	Weak transcription	Fetal Brain Male	brain
21	chr21:40613400-40652000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr21:40613800-40651000	Strong transcription	Fetal Thymus	thymus
23	chr21:40614000-40654400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr21:40614600-40654200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr21:40614800-40635000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr21:40614800-40652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr21:40615800-40639800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr21:40616400-40651800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr21:40617400-40635200	Weak transcription	Colonic Mucosa	Colon
30	chr21:40618000-40659200	Weak transcription	Stomach Mucosa	stomach
31	chr21:40618400-40635400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr21:40619000-40638000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr21:40619400-40656200	Weak transcription	Ovary	ovary
34	chr21:40619600-40635800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr21:40619600-40660200	Weak transcription	Brain Angular Gyrus	brain
36	chr21:40620000-40635200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr21:40620000-40640400	Weak transcription	A549	lung
38	chr21:40620200-40636800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr21:40620400-40635400	Weak transcription	HUVEC	blood vessel
40	chr21:40620800-40636800	Weak transcription	Spleen	Spleen
41	chr21:40622400-40635200	Weak transcription	Brain Substantia Nigra	brain
42	chr21:40622400-40636400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr21:40622600-40634400	Strong transcription	Primary B cells from cord blood	blood
44	chr21:40624000-40642800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr21:40625000-40644000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr21:40625400-40643600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr21:40625800-40639200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr21:40625800-40652400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr21:40626200-40653400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr21:40626400-40637200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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