Variant report

Variant	rs9976233
Chromosome Location	chr21:47616913-47616914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:47616738-47616919	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47614413..47616404-chr21:47616711..47619488,2	K562	blood:
2	chr21:47609281..47613722-chr21:47615252..47618849,4	MCF-7	breast:

Variant related genes	Relation type
LSS	TF binding region
ENSG00000235878	TF binding region
ENSG00000160285	Chromatin interaction
ENSG00000235878	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10854480	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12482209	0.81[ASN][1000 genomes]
rs13046451	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13049175	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13052701	0.81[ASN][1000 genomes]
rs13052806	0.89[ASN][1000 genomes]
rs2001809	0.82[ASN][1000 genomes]
rs2187118	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187120	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187121	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187122	0.94[ASN][1000 genomes]
rs2254524	0.97[ASN][1000 genomes]
rs2277826	0.89[ASN][1000 genomes]
rs2280955	0.88[ASN][1000 genomes]
rs2280956	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280957	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280958	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280959	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2330408	0.96[ASN][1000 genomes]
rs2839139	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2839140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839141	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2839144	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2839145	0.85[ASN][1000 genomes]
rs2839146	0.97[ASN][1000 genomes]
rs2839155	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839157	0.88[ASN][1000 genomes]
rs2839160	0.83[ASN][1000 genomes]
rs2839161	0.83[ASN][1000 genomes]
rs2839167	0.81[ASN][1000 genomes]
rs2968	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35679325	0.90[ASN][1000 genomes]
rs4818828	0.97[ASN][1000 genomes]
rs4819213	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819214	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4819215	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819217	0.88[ASN][1000 genomes]
rs4819218	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55689527	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62212862	0.95[ASN][1000 genomes]
rs6518278	0.88[ASN][1000 genomes]
rs6518282	0.88[ASN][1000 genomes]
rs6518285	0.89[ASN][1000 genomes]
rs7280110	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282841	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs914247	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs915804	0.82[ASN][1000 genomes]
rs9717	0.94[ASN][1000 genomes]
rs9979525	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9984242	0.88[ASN][1000 genomes]
rs9984708	0.83[ASN][1000 genomes]
rs9984986	0.89[ASN][1000 genomes]
rs999691	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
2	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
6	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	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
8	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
9	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv914098	chr21:47467894-47619784	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
17	nsv1061087	chr21:47476088-47643219	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
18	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
19	nsv914101	chr21:47491014-47650362	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
20	nsv914116	chr21:47535248-47650362	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
21	nsv914132	chr21:47572244-47619784	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
22	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
23	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
24	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
25	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
26	nsv1062031	chr21:47608580-47643219	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
27	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9976233	YBEY	cis	Whole Blood	GTEx
rs9976233	C21orf56	Cis_1M	lymphoblastoid	RTeQTL
rs9976233	MCM3AP	cis	Skin Sun Exposed Lower leg	GTEx
rs9976233	MCM3AP-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs9976233	YBEY	cis	Esophagus Mucosa	GTEx
rs9976233	YBEY	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47605000-47633200	Weak transcription	Stomach Mucosa	stomach
2	chr21:47605200-47646200	Weak transcription	Psoas Muscle	Psoas
3	chr21:47605400-47625600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr21:47605400-47646200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr21:47605400-47646200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr21:47605800-47621000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr21:47606600-47639800	Strong transcription	Fetal Brain Female	brain
8	chr21:47607400-47645200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr21:47607400-47646200	Strong transcription	Fetal Stomach	stomach
10	chr21:47607600-47617000	Strong transcription	Brain Germinal Matrix	brain
11	chr21:47607800-47621000	Strong transcription	Liver	Liver
12	chr21:47608400-47621000	Strong transcription	Dnd41	blood
13	chr21:47608400-47622800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr21:47609000-47617000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr21:47609000-47617600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr21:47609000-47634800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr21:47609200-47617000	Strong transcription	Spleen	Spleen
18	chr21:47609200-47621000	Strong transcription	Fetal Muscle Leg	muscle
19	chr21:47609400-47617000	Strong transcription	Aorta	Aorta
20	chr21:47609400-47617200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr21:47609400-47618200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr21:47609400-47618200	Strong transcription	Colonic Mucosa	Colon
23	chr21:47609400-47621400	Weak transcription	A549	lung
24	chr21:47609400-47621600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr21:47609600-47617000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr21:47609600-47617000	Strong transcription	Ovary	ovary
27	chr21:47609600-47623000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr21:47609800-47617000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr21:47609800-47617600	Strong transcription	Brain Cingulate Gyrus	brain
30	chr21:47609800-47620000	Strong transcription	Lung	lung
31	chr21:47609800-47621000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr21:47609800-47621000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr21:47610000-47618200	Strong transcription	Fetal Intestine Small	intestine
34	chr21:47610000-47637600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr21:47610000-47644000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr21:47610200-47617000	Strong transcription	Fetal Intestine Large	intestine
37	chr21:47610200-47618200	Strong transcription	Brain Hippocampus Middle	brain
38	chr21:47610200-47618400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr21:47610200-47621000	Strong transcription	Primary T cells from cord blood	blood
40	chr21:47610800-47617000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr21:47610800-47617600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr21:47610800-47621000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr21:47611000-47617000	Strong transcription	Rectal Smooth Muscle	rectum
44	chr21:47611000-47617400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr21:47611000-47633600	Weak transcription	Right Atrium	heart
46	chr21:47611200-47622000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr21:47611600-47617000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr21:47611600-47617000	Strong transcription	Right Ventricle	heart
49	chr21:47611600-47617200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr21:47611600-47619400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links