Variant report

Variant	rs9984420
Chromosome Location	chr21:45199112-45199113
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr21:45198823-45199136	K562	blood:	n/a	n/a
2	POLR2A	chr21:45198463-45199230	U87	brain:	n/a	n/a
3	JUND	chr21:45199063-45199121	K562	blood:	n/a	n/a
4	POLR2A	chr21:45198749-45199181	K562	blood:	n/a	n/a
5	SPI1	chr21:45198765-45199125	GM12891	blood:	n/a	n/a
6	SP1	chr21:45198664-45199357	HCT-116	colon:	n/a	n/a
7	ELF1	chr21:45198584-45199210	K562	blood:	n/a	n/a
8	SPI1	chr21:45198763-45199169	GM12878	blood:	n/a	n/a
9	SPI1	chr21:45198764-45199332	HL-60	blood:	n/a	n/a
10	SPI1	chr21:45198706-45199220	GM12878	blood:	n/a	n/a
11	POLR2A	chr21:45198931-45199152	HepG2	liver:	n/a	n/a
12	SPI1	chr21:45198752-45199151	K562	blood:	n/a	n/a
13	SPI1	chr21:45198794-45199228	HL-60	blood:	n/a	n/a
14	POLR2A	chr21:45198484-45199230	U87	brain:	n/a	n/a
15	MAZ	chr21:45198795-45199117	K562	blood:	n/a	n/a
16	EP300	chr21:45198966-45199128	K562	blood:	n/a	n/a
17	IKZF1	chr21:45198939-45199123	GM12878	blood:	n/a	n/a
18	SPI1	chr21:45198807-45199158	GM12891	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:45199094-45199144	HRE	kidney:	n/a
2	chr21:45199094-45199144	NT2-D1	testis:	n/a
3	chr21:45199094-45199144	PFSK-1	brain:	n/a
4	chr21:45199094-45199144	AG09309	skin:	n/a
5	chr21:45199094-45199144	ovcar-3	ovarian:	n/a
6	chr21:45199094-45199144	PrEC	prostate:	n/a
7	chr21:45199094-45199144	IMR90	lung:	fetal
8	chr21:45199094-45199144	AoSMC	blood vessel:	n/a
9	chr21:45199094-45199144	HRPEpiC	eye:	n/a
10	chr21:45199094-45199144	HCF	heart:	n/a
11	chr21:45199094-45199144	K562	blood:	n/a
12	chr21:45199094-45199144	NHBE	bronchial:	n/a
13	chr21:45199094-45199144	SK-N-SH	brain:	n/a
14	chr21:45199094-45199144	GM12892	blood:	n/a
15	chr21:45199094-45199144	NHDF-neo	bronchial:	n/a
16	chr21:45199094-45199144	GM19239	blood:	n/a
17	chr21:45199094-45199144	MCF10A-Er-Src	breast:	n/a
18	chr21:45199094-45199144	SKMC	muscle:	n/a
19	chr21:45199094-45199144	HRCEpiC	kidney:	n/a
20	chr21:45199094-45199144	Hepatocyte	liver:	n/a
21	chr21:45199094-45199144	HUVEC	blood vessel:	n/a
22	chr21:45199094-45199144	NB4	blood:	n/a
23	chr21:45199094-45199144	NH-A	brain:	n/a
24	chr21:45199094-45199144	T-47D	breast:	n/a
25	chr21:45199094-45199144	Caco-2	colon:	n/a
26	chr21:45199094-45199144	CMK	blood:	n/a
27	chr21:45199094-45199144	SK-N-SH_RA	brain:	n/a
28	chr21:45199094-45199144	H1-hESC	embryonic stem cell:	embryo
29	chr21:45199094-45199144	HEEpiC	esophagus:	n/a
30	chr21:45199094-45199144	AG04450	lung:	fetal
31	chr21:45199094-45199144	HPAEpiC	pulmonary alveolar:	n/a
32	chr21:45199094-45199144	ProgFib	skin:	n/a
33	chr21:45199094-45199144	AG09319	gingival:	n/a
34	chr21:45199094-45199144	A549	lung:	n/a
35	chr21:45199094-45199144	SK-N-MC	brain:	n/a
36	chr21:45199094-45199144	Jurkat	blood:	n/a
37	chr21:45199094-45199144	HCPEpiC	choroid plexus:	n/a
38	chr21:45199094-45199144	HEK293	kidney:	embryo
39	chr21:45199094-45199144	ECC-1	luminal epithelium:	n/a
40	chr21:45199094-45199144	AG10803	skin:	n/a
41	chr21:45199094-45199144	AG04449	skin:	fetal
42	chr21:45199094-45199144	SAEC	small airway:	n/a
43	chr21:45199094-45199144	LNCaP	prostate:	n/a
44	chr21:45199094-45199144	HCT-116	colon:	n/a
45	chr21:45199094-45199144	Hela-S3	cervix:	n/a
46	chr21:45199094-45199144	HL-60	blood:	n/a
47	chr21:45199094-45199144	U87	brain:	n/a
48	chr21:45199094-45199144	HepG2	liver:	n/a
49	chr21:45199094-45199144	HIPEpiC	eye:	n/a
50	chr21:45199094-45199144	GM12891	blood:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45195296..45199656-chr21:45201104..45204314,12	MCF-7	breast:
2	chr21:45137876..45142347-chr21:45194759..45200624,9	MCF-7	breast:
3	chr21:45138069..45142004-chr21:45192681..45200004,8	MCF-7	breast:
4	chr21:45166127..45168190-chr21:45198985..45201869,2	K562	blood:

No data

Variant related genes	Relation type
CSTB	TF binding region
TMEM97P1	TF binding region
CSTB	CpG island
TMEM97P1	CpG island
ENSG00000160209	Chromatin interaction
ENSG00000234030	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11089097	0.83[ASN][1000 genomes]
rs11909278	0.83[ASN][1000 genomes]
rs1537118	0.96[ASN][1000 genomes]
rs1537120	0.96[ASN][1000 genomes]
rs2070538	0.95[ASN][1000 genomes]
rs2838364	0.96[ASN][1000 genomes]
rs2838373	0.98[ASN][1000 genomes]
rs2838380	0.94[ASN][1000 genomes]
rs2838385	0.85[ASN][1000 genomes]
rs2838391	0.83[ASN][1000 genomes]
rs28759507	0.99[ASN][1000 genomes]
rs4819314	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55663506	0.83[ASN][1000 genomes]
rs55825369	0.83[ASN][1000 genomes]
rs55982230	0.83[ASN][1000 genomes]
rs56387943	0.81[ASN][1000 genomes]
rs60418573	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62230077	0.81[ASN][1000 genomes]
rs6369	0.84[EUR][1000 genomes]
rs6518321	0.97[ASN][1000 genomes]
rs67676705	0.97[ASN][1000 genomes]
rs8128323	0.96[ASN][1000 genomes]
rs915770	0.85[ASN][1000 genomes]
rs9976535	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9980220	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv913876	chr21:45119629-45267193	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2830066	chr21:45133868-45258047	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv913879	chr21:45145286-45237039	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv913880	chr21:45145286-45263920	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv913881	chr21:45145286-45267193	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
8	nsv1055154	chr21:45148076-45203162	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic 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	22 gene(s)	inside rSNPs	diseases
9	nsv470904	chr21:45151045-45258047	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
11	nsv834107	chr21:45155325-45294546	Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	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
13	nsv520305	chr21:45175958-45246326	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv913883	chr21:45191139-45252838	Weak transcription Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv913884	chr21:45191139-45255836	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv544469	chr21:45194085-45257959	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9984420	CSTB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45196800-45199400	Enhancers	Primary T cells fromperipheralblood	blood
2	chr21:45196800-45199600	Weak transcription	Right Ventricle	heart
3	chr21:45196800-45199800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr21:45196800-45200600	Weak transcription	NHEK	skin
5	chr21:45196800-45201000	Weak transcription	Fetal Intestine Large	intestine
6	chr21:45196800-45202000	Weak transcription	Liver	Liver
7	chr21:45196800-45203000	Weak transcription	Lung	lung
8	chr21:45196800-45206400	Weak transcription	Gastric	stomach
9	chr21:45196800-45206400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr21:45196800-45208800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr21:45196800-45209000	Weak transcription	Aorta	Aorta
12	chr21:45197000-45200000	Enhancers	Dnd41	blood
13	chr21:45197000-45200800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr21:45197400-45200000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:45197600-45199200	Enhancers	K562	blood
16	chr21:45197600-45200000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr21:45197800-45199200	Enhancers	Primary T cells from cord blood	blood
18	chr21:45197800-45199800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr21:45198000-45199200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr21:45198000-45199200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr21:45198000-45199200	Flanking Active TSS	HepG2	liver
22	chr21:45198000-45199200	Enhancers	HMEC	breast
23	chr21:45198000-45199400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr21:45198000-45199800	Enhancers	Fetal Thymus	thymus
25	chr21:45198000-45200000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr21:45198200-45199200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr21:45198200-45199200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr21:45198200-45199400	Enhancers	Primary B cells from cord blood	blood
29	chr21:45198200-45200800	Enhancers	GM12878-XiMat	blood
30	chr21:45198400-45199200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr21:45198400-45199200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr21:45198400-45199200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr21:45198400-45199400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr21:45198400-45199400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr21:45198400-45200000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr21:45198600-45199200	Enhancers	Primary B cells from peripheral blood	blood
37	chr21:45198600-45199200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr21:45198600-45199400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr21:45198600-45199400	Enhancers	Adipose Nuclei	Adipose
40	chr21:45198800-45199200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr21:45198800-45199600	Active TSS	Esophagus	oesophagus
42	chr21:45198800-45200800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr21:45198800-45206400	Weak transcription	Spleen	Spleen
44	chr21:45198800-45206600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr21:45199000-45199200	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr21:45199000-45199200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr21:45199000-45199200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr21:45199000-45199200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr21:45199000-45199400	Enhancers	Colonic Mucosa	Colon
50	chr21:45199000-45200400	Weak transcription	Placenta	Placenta

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