Variant report

Variant	rs9941787
Chromosome Location	chr21:45116042-45116043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45109608..45112667-chr21:45115879..45118548,4	K562	blood:
2	chr21:45079803..45081678-chr21:45114848..45116362,2	MCF-7	breast:
3	chr21:45112710..45116467-chr21:45117620..45123990,9	K562	blood:
4	chr21:45109608..45111487-chr21:45115879..45118548,2	K562	blood:

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10211901	0.87[EUR][1000 genomes]
rs1041455	0.82[LWK][hapmap];0.83[YRI][hapmap]
rs1073522	0.81[CEU][hapmap];0.87[YRI][hapmap]
rs10854486	0.82[EUR][1000 genomes]
rs11089092	0.81[EUR][1000 genomes]
rs11089093	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1122873	0.84[CEU][hapmap];0.87[YRI][hapmap]
rs11700909	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11700913	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11702544	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11909064	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12165286	0.84[YRI][hapmap]
rs13051953	0.96[EUR][1000 genomes]
rs1378079	0.82[CHD][hapmap]
rs1378080	0.82[YRI][hapmap]
rs141521	0.82[CHD][hapmap]
rs1454648	0.84[CEU][hapmap]
rs1454650	0.81[ASW][hapmap];0.85[CEU][hapmap];0.82[CHD][hapmap];0.86[TSI][hapmap]
rs1454651	0.85[CEU][hapmap]
rs1584917	0.85[CEU][hapmap]
rs1584918	0.85[CEU][hapmap]
rs1598206	0.82[CHD][hapmap]
rs162344	0.82[CHD][hapmap]
rs162366	0.87[ASW][hapmap];0.82[CHD][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap]
rs162372	0.82[YRI][hapmap]
rs162375	0.87[ASW][hapmap];0.82[CHD][hapmap];0.81[LWK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs162376	0.87[ASW][hapmap];0.82[CHD][hapmap];0.84[TSI][hapmap]
rs162377	0.81[ASW][hapmap];0.82[CHD][hapmap];0.82[YRI][hapmap]
rs162380	0.82[YRI][hapmap]
rs162390	0.82[YRI][hapmap]
rs162398	0.82[CHD][hapmap]
rs162399	0.82[YRI][hapmap]
rs162400	0.87[ASW][hapmap];0.82[CHD][hapmap];0.82[LWK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap]
rs2006113	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2051407	0.85[EUR][1000 genomes]
rs2070533	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2155722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2186924	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2236665	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236666	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236667	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246602	0.81[CEU][hapmap];0.82[CHD][hapmap]
rs2250773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2282526	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs229357	0.81[CEU][hapmap];0.87[YRI][hapmap]
rs2298561	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2298562	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2329442	0.87[ASW][hapmap];0.85[CEU][hapmap];0.82[CHD][hapmap];0.82[LWK][hapmap];0.86[TSI][hapmap]
rs2329593	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2838316	0.82[CHD][hapmap];0.85[LWK][hapmap];0.87[YRI][hapmap]
rs2838320	0.87[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap]
rs2838324	0.81[CEU][hapmap];0.87[YRI][hapmap]
rs2838331	0.85[CEU][hapmap];0.82[CHD][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap]
rs2838337	0.87[YRI][hapmap]
rs2838338	0.85[CEU][hapmap]
rs2838339	0.85[CEU][hapmap];0.82[CHD][hapmap];0.85[LWK][hapmap];0.87[YRI][hapmap]
rs2838344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838345	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838348	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838350	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838351	0.81[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838353	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838354	0.86[CHB][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3819161	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs389278	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs4818858	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4818859	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818860	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818861	0.94[EUR][1000 genomes]
rs4819219	0.87[YRI][hapmap]
rs4819270	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs4819283	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4819285	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819286	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819287	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819288	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819289	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819290	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4819291	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4819292	0.96[EUR][1000 genomes]
rs4819293	0.94[EUR][1000 genomes]
rs4819294	0.95[EUR][1000 genomes]
rs4819295	0.93[JPT][hapmap]
rs4819296	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs6518302	0.87[ASW][hapmap];0.85[CEU][hapmap];0.82[CHD][hapmap];0.85[LWK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap]
rs6518310	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs7276215	0.81[CEU][hapmap];0.87[YRI][hapmap]
rs7276633	0.81[CEU][hapmap]
rs7277539	0.87[ASW][hapmap];0.84[CEU][hapmap];0.82[CHD][hapmap];0.82[LWK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs7279959	0.92[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7282122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7282405	0.97[EUR][1000 genomes]
rs7283428	0.95[EUR][1000 genomes]
rs762400	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8129601	0.89[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8131027	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs8131111	0.95[EUR][1000 genomes]
rs8133276	0.96[EUR][1000 genomes]
rs8133523	0.84[CEU][hapmap];0.87[YRI][hapmap]
rs914197	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs914198	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9306159	0.85[CEU][hapmap]
rs9306160	0.96[CEU][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs969060	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9977076	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9978403	0.82[YRI][hapmap]
rs9978858	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9978934	0.91[YRI][hapmap]
rs9979935	0.91[YRI][hapmap]
rs9980185	0.83[CEU][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap]
rs9981291	0.87[ASW][hapmap];0.85[CEU][hapmap];0.82[CHD][hapmap];0.86[TSI][hapmap]
rs9981790	0.82[CHB][hapmap]
rs9982727	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9983670	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9983752	0.82[LWK][hapmap];0.87[YRI][hapmap]
rs9983763	0.82[CHD][hapmap]

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	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv913874	chr21:45041790-45191005	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv531544	chr21:45071371-45202912	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1066728	chr21:45089877-45131723	Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1066613	chr21:45108233-45148136	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9941787	C21orf57	cis	parietal	SCAN
rs9941787	HSF2BP	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45080600-45122400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:45080800-45121800	Weak transcription	Fetal Heart	heart
3	chr21:45080800-45122600	Weak transcription	Small Intestine	intestine
4	chr21:45082800-45116600	Strong transcription	Primary T cells from cord blood	blood
5	chr21:45086000-45117200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:45088400-45117200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr21:45088600-45116400	Strong transcription	Dnd41	blood
8	chr21:45088600-45117000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr21:45088800-45118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:45089000-45117000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr21:45089000-45117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr21:45089000-45117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr21:45089200-45116200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr21:45089200-45117000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr21:45089200-45117200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr21:45089400-45116600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr21:45089600-45116400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr21:45089600-45116400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr21:45089800-45117000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr21:45089800-45117200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr21:45093800-45117000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr21:45094000-45117600	Strong transcription	Fetal Intestine Small	intestine
23	chr21:45094200-45116200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr21:45094600-45116200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr21:45094600-45116600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr21:45094600-45117200	Strong transcription	Fetal Stomach	stomach
27	chr21:45094800-45116400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr21:45094800-45117200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr21:45094800-45122000	Weak transcription	Right Atrium	heart
30	chr21:45095200-45116400	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr21:45095400-45117000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr21:45099200-45116200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr21:45100000-45116400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr21:45100000-45116800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr21:45100000-45117200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr21:45100200-45117000	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr21:45100400-45116800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr21:45100600-45116600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr21:45100800-45117600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr21:45101200-45117200	Strong transcription	Liver	Liver
41	chr21:45101400-45116600	Strong transcription	Left Ventricle	heart
42	chr21:45101800-45116400	Strong transcription	Brain Germinal Matrix	brain
43	chr21:45101800-45116400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr21:45101800-45116800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr21:45101800-45116800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr21:45101800-45117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr21:45102000-45116600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr21:45102200-45116400	Strong transcription	NHEK	skin
49	chr21:45102200-45117000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr21:45102400-45116600	Strong transcription	Ovary	ovary

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