Variant report

Variant	rs9978397
Chromosome Location	chr21:47798157-47798158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47797361..47799888-chr21:47812177..47813835,2	K562	blood:
2	chr21:47796873..47800064-chr21:47803863..47807599,5	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10222102	0.97[ASN][1000 genomes]
rs13047209	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13048286	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1543756	0.83[ASN][1000 genomes]
rs1974172	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2073378	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28385599	0.98[ASN][1000 genomes]
rs2839226	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2839227	0.89[ASN][1000 genomes]
rs2839228	0.87[ASN][1000 genomes]
rs2839232	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2839234	0.98[ASN][1000 genomes]
rs2839235	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2839240	0.91[ASN][1000 genomes]
rs28716675	0.98[ASN][1000 genomes]
rs34950974	0.98[ASN][1000 genomes]
rs35274838	0.88[ASN][1000 genomes]
rs35370178	0.86[ASN][1000 genomes]
rs35449415	0.98[ASN][1000 genomes]
rs3788258	0.96[ASN][1000 genomes]
rs3788261	0.94[ASN][1000 genomes]
rs3788263	0.92[ASN][1000 genomes]
rs3788264	0.91[ASN][1000 genomes]
rs4818837	0.87[ASN][1000 genomes]
rs4818840	0.91[ASN][1000 genomes]
rs4819240	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4819241	0.80[ASN][1000 genomes]
rs4819242	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4819244	0.91[ASN][1000 genomes]
rs6518289	0.87[ASN][1000 genomes]
rs6518291	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71326324	0.84[ASN][1000 genomes]
rs7279052	0.85[ASN][1000 genomes]
rs7279204	0.85[ASN][1000 genomes]
rs7279344	0.94[ASN][1000 genomes]
rs7281373	0.91[ASN][1000 genomes]
rs7281777	0.87[ASN][1000 genomes]
rs8131546	0.84[ASN][1000 genomes]
rs9306152	0.88[ASN][1000 genomes]
rs9637173	0.87[ASN][1000 genomes]
rs9980404	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9981170	0.97[ASN][1000 genomes]
rs9984599	0.85[ASN][1000 genomes]
rs9984689	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
2	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
3	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
4	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
5	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
6	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
7	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
9	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
10	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
11	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
12	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
13	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS 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	83 gene(s)	inside rSNPs	n/a
14	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
15	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
16	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
17	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
18	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
19	nsv587975	chr21:47661235-47830843	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
20	nsv432159	chr21:47673247-47854392	Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
21	nsv527355	chr21:47678774-47863025	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
22	nsv914136	chr21:47681041-47900994	Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	n/a
23	nsv914137	chr21:47700498-47862624	Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
24	nsv914138	chr21:47700498-47866227	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
25	nsv914140	chr21:47712185-47866227	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a
26	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
27	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
28	nsv914142	chr21:47772468-47866227	Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
29	nsv1062683	chr21:47788763-47851236	Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
30	nsv914143	chr21:47792874-47862624	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
31	nsv914144	chr21:47792874-47866227	Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9978397	YBEY	cis	Thyroid	GTEx
rs9978397	YBEY	cis	Skin Sun Exposed Lower leg	GTEx
rs9978397	YBEY	cis	Esophagus Muscularis	GTEx
rs9978397	C21orf57	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47764200-47800200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr21:47765400-47798400	Strong transcription	Stomach Smooth Muscle	stomach
3	chr21:47774200-47801400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr21:47775600-47857600	Weak transcription	Stomach Mucosa	stomach
5	chr21:47786200-47802800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr21:47787200-47813200	Weak transcription	NH-A	brain
7	chr21:47787400-47817000	Weak transcription	Small Intestine	intestine
8	chr21:47787800-47813600	Weak transcription	Colon Smooth Muscle	Colon
9	chr21:47788000-47813000	Weak transcription	NHDF-Ad	bronchial
10	chr21:47788000-47813600	Weak transcription	HUVEC	blood vessel
11	chr21:47789000-47802200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr21:47789400-47807200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr21:47789400-47842600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr21:47789800-47804800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr21:47789800-47805600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr21:47789800-47809000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr21:47790000-47822000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr21:47790400-47805800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr21:47790600-47805800	Weak transcription	Colonic Mucosa	Colon
20	chr21:47790800-47799800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr21:47790800-47800000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr21:47791400-47799600	Strong transcription	Primary T cells from cord blood	blood
23	chr21:47791400-47800000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr21:47791600-47800000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr21:47792000-47799800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr21:47792200-47801800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr21:47792200-47804600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr21:47792200-47812800	Weak transcription	Fetal Brain Male	brain
29	chr21:47792400-47798200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr21:47792400-47798400	Weak transcription	GM12878-XiMat	blood
31	chr21:47792400-47800600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr21:47792400-47800800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr21:47792400-47801200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr21:47792400-47801200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr21:47792400-47801200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr21:47792400-47801200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr21:47792400-47801200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr21:47792400-47801200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr21:47792400-47801200	Weak transcription	Brain Hippocampus Middle	brain
40	chr21:47792400-47801200	Weak transcription	Brain Substantia Nigra	brain
41	chr21:47792400-47801600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr21:47792400-47801600	Weak transcription	Primary B cells from cord blood	blood
43	chr21:47792400-47801600	Weak transcription	Liver	Liver
44	chr21:47792400-47801800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr21:47792400-47801800	Weak transcription	Adipose Nuclei	Adipose
46	chr21:47792400-47801800	Weak transcription	Aorta	Aorta
47	chr21:47792400-47801800	Weak transcription	Fetal Kidney	kidney
48	chr21:47792400-47801800	Weak transcription	Pancreas	Pancrea
49	chr21:47792400-47802000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr21:47792400-47804400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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