Variant report

Variant	rs2020947
Chromosome Location	chr21:45452249-45452250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 160 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs1059813	0.84[EUR][1000 genomes]
rs10854489	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089111	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1131999	0.85[ASN][1000 genomes]
rs11700840	0.81[EUR][1000 genomes]
rs11700919	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12627239	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13047030	0.84[EUR][1000 genomes]
rs13050630	0.89[ASN][1000 genomes]
rs1858665	0.86[EUR][1000 genomes]
rs2020945	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2020946	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2020948	0.91[ASN][1000 genomes]
rs2039272	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2051260	0.84[EUR][1000 genomes]
rs2071142	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2071143	0.84[EUR][1000 genomes]
rs2071146	0.84[EUR][1000 genomes]
rs2071147	0.84[EUR][1000 genomes]
rs2071152	0.86[ASN][1000 genomes]
rs2073432	0.83[EUR][1000 genomes]
rs2073433	0.84[EUR][1000 genomes]
rs2073435	0.85[EUR][1000 genomes]
rs2156428	0.89[ASN][1000 genomes]
rs2238704	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238705	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238706	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238707	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238708	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2238709	0.95[ASN][1000 genomes]
rs2238710	1.00[ASN][1000 genomes]
rs2238711	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2238712	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2238713	0.84[EUR][1000 genomes]
rs2242950	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2242953	0.85[EUR][1000 genomes]
rs2242954	0.81[EUR][1000 genomes]
rs2243348	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2243999	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2245372	0.88[ASN][1000 genomes]
rs2245380	0.89[ASN][1000 genomes]
rs2245386	0.88[ASN][1000 genomes]
rs2245462	0.88[ASN][1000 genomes]
rs2245759	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247400	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2251267	0.84[EUR][1000 genomes]
rs2255716	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255828	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255922	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2255955	0.89[EUR][1000 genomes]
rs2256392	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256441	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276530	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277805	0.84[EUR][1000 genomes]
rs2277806	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2299812	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299813	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299815	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299818	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2299820	0.88[ASN][1000 genomes]
rs2329707	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2516519	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2516521	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2776368	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2838466	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838467	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2838468	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838469	0.89[EUR][1000 genomes]
rs2838471	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838472	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2838473	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838474	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838476	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838477	0.91[ASN][1000 genomes]
rs2838478	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838480	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838481	0.89[ASN][1000 genomes]
rs2838482	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838483	0.89[ASN][1000 genomes]
rs2838485	0.88[ASN][1000 genomes]
rs2838486	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2838488	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838489	0.84[EUR][1000 genomes]
rs2838490	0.85[EUR][1000 genomes]
rs2838491	0.84[EUR][1000 genomes]
rs2838492	0.84[EUR][1000 genomes]
rs2838494	0.83[EUR][1000 genomes]
rs2838496	0.84[EUR][1000 genomes]
rs2838498	0.83[EUR][1000 genomes]
rs2838499	0.84[EUR][1000 genomes]
rs2838502	0.81[EUR][1000 genomes]
rs2850150	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850155	0.87[EUR][1000 genomes]
rs2850156	0.85[EUR][1000 genomes]
rs2850157	0.85[EUR][1000 genomes]
rs2855651	0.86[EUR][1000 genomes]
rs2855652	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28859288	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35538274	0.82[EUR][1000 genomes]
rs35610725	0.89[ASN][1000 genomes]
rs3788097	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3788098	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3788101	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3788104	0.81[EUR][1000 genomes]
rs4818878	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818881	0.84[EUR][1000 genomes]
rs4819366	0.98[ASN][1000 genomes]
rs4819370	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4819372	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819373	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4819376	0.85[EUR][1000 genomes]
rs4819377	0.84[EUR][1000 genomes]
rs4819378	0.83[EUR][1000 genomes]
rs4819379	0.84[EUR][1000 genomes]
rs4819381	0.83[EUR][1000 genomes]
rs56384549	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62229738	0.83[EUR][1000 genomes]
rs7277269	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7279319	0.81[EUR][1000 genomes]
rs7279727	0.98[ASN][1000 genomes]
rs7280581	0.84[EUR][1000 genomes]
rs7281270	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7281291	0.81[EUR][1000 genomes]
rs7281768	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7281778	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7282643	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729882	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs756553	0.84[EUR][1000 genomes]
rs756554	0.82[EUR][1000 genomes]
rs756555	0.84[EUR][1000 genomes]
rs8126564	0.83[EUR][1000 genomes]
rs8126754	1.00[ASN][1000 genomes]
rs8126958	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs8129971	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130647	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8132918	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8133422	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8133610	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs915878	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9306171	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9306172	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9306174	0.88[ASN][1000 genomes]
rs9680179	0.83[EUR][1000 genomes]
rs968714	0.84[EUR][1000 genomes]
rs9974165	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974315	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9975708	0.88[ASN][1000 genomes]
rs9975978	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9977564	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9978130	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979882	0.82[EUR][1000 genomes]
rs9981257	0.86[ASN][1000 genomes]
rs9981485	0.86[EUR][1000 genomes]
rs9982663	0.98[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	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1063752	chr21:45406095-45460342	Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv459293	chr21:45415913-45555079	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv587721	chr21:45415913-45555079	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1064549	chr21:45446358-45493720	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2020947	PWP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45433200-45452600	Weak transcription	Aorta	Aorta
2	chr21:45441800-45452400	Weak transcription	Fetal Brain Female	brain
3	chr21:45444400-45452400	Weak transcription	Fetal Intestine Small	intestine
4	chr21:45445200-45452400	Weak transcription	Esophagus	oesophagus
5	chr21:45445200-45454400	Weak transcription	A549	lung
6	chr21:45445200-45454600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr21:45445200-45457800	Weak transcription	Small Intestine	intestine
8	chr21:45445200-45471400	Weak transcription	Stomach Mucosa	stomach
9	chr21:45445400-45454400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr21:45445400-45454600	Weak transcription	Colonic Mucosa	Colon
11	chr21:45445400-45509400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr21:45445600-45452600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr21:45445800-45452800	Weak transcription	Fetal Lung	lung
14	chr21:45445800-45457800	Weak transcription	Gastric	stomach
15	chr21:45445800-45458200	Weak transcription	HSMMtube	muscle
16	chr21:45445800-45471400	Weak transcription	Right Atrium	heart
17	chr21:45446000-45452400	Weak transcription	Fetal Muscle Leg	muscle
18	chr21:45446000-45452600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr21:45446000-45452600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr21:45446000-45452600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr21:45446000-45452600	Weak transcription	HSMM	muscle
22	chr21:45446000-45452600	Weak transcription	HUVEC	blood vessel
23	chr21:45446200-45452400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr21:45446200-45452400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr21:45446200-45452400	Weak transcription	HMEC	breast
26	chr21:45446200-45452600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr21:45446200-45452600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr21:45446200-45452800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr21:45446200-45453000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr21:45446200-45453800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr21:45446200-45454200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr21:45446200-45454400	Weak transcription	Colon Smooth Muscle	Colon
33	chr21:45446200-45454600	Weak transcription	NHLF	lung
34	chr21:45446400-45452400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr21:45446400-45452600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr21:45446400-45452600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr21:45446400-45452600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr21:45446400-45453400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr21:45446400-45454600	Weak transcription	Fetal Kidney	kidney
40	chr21:45446400-45502200	Weak transcription	Fetal Heart	heart
41	chr21:45446600-45452600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr21:45446600-45452600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr21:45446600-45452600	Weak transcription	NH-A	brain
44	chr21:45446600-45454600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr21:45446600-45479600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr21:45446800-45452400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr21:45446800-45452400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr21:45446800-45452600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr21:45446800-45452600	Weak transcription	Placenta	Placenta
50	chr21:45446800-45453800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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