Variant report

Variant	rs2838435
Chromosome Location	chr21:45341854-45341855
allele	G/T
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	RELA	chr21:45341231-45342365	GM19099	blood:	n/a	n/a
2	JUND	chr21:45341845-45342164	HepG2	liver:	n/a	chr21:45342015-45342024 chr21:45342015-45342025 chr21:45342014-45342025 chr21:45342014-45342026 chr21:45342016-45342025
3	ZNF384	chr21:45341573-45342252	K562	blood:	n/a	n/a
4	RUNX3	chr21:45341304-45342451	GM12878	blood:	n/a	n/a
5	NFATC1	chr21:45341768-45342458	GM12878	blood:	n/a	chr21:45341966-45341980
6	EBF1	chr21:45341171-45342328	GM12878	blood:	n/a	chr21:45341827-45341836 chr21:45341684-45341693 chr21:45341827-45341836 chr21:45341682-45341693
7	MYC	chr21:45341765-45342560	K562	blood:	n/a	chr21:45342074-45342084 chr21:45342015-45342024 chr21:45342074-45342089 chr21:45342075-45342086
8	ATF3	chr21:45341812-45342333	K562	blood:	n/a	n/a
9	MYC	chr21:45341784-45342550	K562	blood:	n/a	chr21:45342074-45342084 chr21:45342015-45342024 chr21:45342074-45342089 chr21:45342075-45342086
10	EP300	chr21:45341614-45342390	K562	blood:	n/a	chr21:45342015-45342024
11	USF1	chr21:45341804-45342412	K562	blood:	n/a	n/a
12	MAZ	chr21:45341843-45342428	K562	blood:	n/a	chr21:45342015-45342024 chr21:45342074-45342089 chr21:45342075-45342086
13	MAX	chr21:45341850-45342810	H1-hESC	embryonic stem cell:	n/a	chr21:45342074-45342084 chr21:45342015-45342024 chr21:45342074-45342089 chr21:45342075-45342086
14	POLR2A	chr21:45341816-45342456	K562	blood:	n/a	n/a
15	MTA3	chr21:45340954-45342916	GM12878	blood:	n/a	n/a
16	EP300	chr21:45341275-45342418	GM12878	blood:	n/a	chr21:45342015-45342024
17	FOXM1	chr21:45341781-45342453	GM12878	blood:	n/a	n/a
18	CHD2	chr21:45341232-45342527	GM12878	blood:	n/a	n/a
19	SMC3	chr21:45341431-45342376	GM12878	blood:	n/a	n/a
20	EBF1	chr21:45341130-45342390	GM12878	blood:	n/a	chr21:45341827-45341836 chr21:45341684-45341693 chr21:45341827-45341836 chr21:45341682-45341693
21	TBL1XR1	chr21:45341410-45342340	GM12878	blood:	n/a	n/a
22	PML	chr21:45341818-45342432	K562	blood:	n/a	chr21:45342014-45342023
23	ZC3H11A	chr21:45341773-45342257	K562	blood:	n/a	n/a
24	POLR2A	chr21:45341762-45342817	K562	blood:	n/a	n/a
25	STAT5A	chr21:45341622-45342532	GM12878	blood:	n/a	chr21:45342016-45342025 chr21:45341982-45341993
26	CBX3	chr21:45341728-45342774	K562	blood:	n/a	n/a
27	RCOR1	chr21:45341829-45342299	K562	blood:	n/a	n/a
28	SP1	chr21:45341555-45342479	GM12878	blood:	n/a	n/a
29	TRIM28	chr21:45341781-45342426	K562	blood:	n/a	chr21:45342014-45342023
30	SPI1	chr21:45341812-45342347	GM12878	blood:	n/a	chr21:45342007-45342020
31	E2F6	chr21:45341808-45342704	K562	blood:	n/a	n/a
32	POLR2A	chr21:45340945-45342783	GM12878	blood:	n/a	n/a
33	ARID3A	chr21:45341826-45342310	K562	blood:	n/a	n/a
34	EGR1	chr21:45341839-45342402	K562	blood:	n/a	chr21:45342214-45342223 chr21:45342155-45342169 chr21:45342157-45342167
35	BCLAF1	chr21:45341749-45342464	GM12878	blood:	n/a	chr21:45341822-45341830
36	EBF1	chr21:45341152-45342483	GM12878	blood:	n/a	chr21:45341827-45341836 chr21:45341684-45341693 chr21:45341827-45341836 chr21:45341682-45341693
37	POLR2A	chr21:45341849-45343205	K562	blood:	n/a	n/a
38	MEF2A	chr21:45341627-45342370	GM12878	blood:	n/a	chr21:45342016-45342024
39	STAT1	chr21:45341305-45342298	GM12878	blood:	n/a	chr21:45342016-45342025 chr21:45341982-45341993
40	MXI1	chr21:45341740-45342334	K562	blood:	n/a	n/a
41	RCOR1	chr21:45341333-45342352	GM12878	blood:	n/a	n/a
42	POLR2A	chr21:45341340-45342450	GM12878	blood:	n/a	n/a
43	MAZ	chr21:45341432-45342440	GM12878	blood:	n/a	chr21:45342015-45342024 chr21:45342074-45342089 chr21:45342075-45342086
44	USF2	chr21:45341240-45342444	GM12878	blood:	n/a	n/a
45	SRF	chr21:45341852-45342173	GM12878	blood:	n/a	chr21:45341983-45342001 chr21:45341980-45341997 chr21:45341942-45341959 chr21:45341982-45341996 chr21:45341944-45341958 chr21:45341949-45341958 chr21:45341982-45342000 chr21:45341945-45341963 chr21:45341948-45341959 chr21:45341947-45341960 chr21:45341947-45341960 chr21:45341985-45341998
46	JUN	chr21:45341841-45342284	K562	blood:	n/a	chr21:45342015-45342024 chr21:45342015-45342025 chr21:45342014-45342026 chr21:45342016-45342025
47	NR2F2	chr21:45341667-45342688	K562	blood:	n/a	n/a
48	PAX5	chr21:45341840-45342519	GM12878	blood:	n/a	n/a
49	MAX	chr21:45341700-45342818	K562	blood:	n/a	chr21:45342074-45342084 chr21:45342015-45342024 chr21:45342074-45342089 chr21:45342075-45342086
50	TBL1XR1	chr21:45341691-45342286	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:45320627..45322266-chr21:45340238..45342463,2	MCF-7	breast:
2	chr21:45340959..45342900-chr21:45429415..45431633,2	K562	blood:
3	chr21:45340526..45342218-chr21:45368922..45371693,3	K562	blood:
4	chr21:45341019..45344772-chr21:45346724..45351005,5	MCF-7	breast:
5	chr21:45280312..45282784-chr21:45340621..45342718,2	K562	blood:
6	chr21:45277545..45279138-chr21:45340639..45343236,2	K562	blood:
7	chr21:45283298..45287513-chr21:45338855..45343382,5	K562	blood:
8	chr21:45302191..45305898-chr21:45340704..45344205,3	K562	blood:
9	chr21:45284242..45287080-chr21:45339493..45341946,2	MCF-7	breast:
10	chr21:45340007..45343701-chr21:45343921..45347389,3	MCF-7	breast:
11	chr21:45228155..45231014-chr21:45339166..45342042,3	K562	blood:
12	chr21:45334570..45338840-chr21:45339112..45343099,4	MCF-7	breast:
13	chr21:45274690..45277191-chr21:45341679..45344447,2	K562	blood:
14	chr21:45341393..45343529-chr21:45348103..45349848,2	MCF-7	breast:
15	chr21:45244325..45246343-chr21:45341504..45344218,2	K562	blood:
16	chr21:45340582..45343200-chr21:45355048..45357219,2	MCF-7	breast:
17	chr21:45283663..45287678-chr21:45338795..45345768,12	K562	blood:
18	chr21:45194660..45196232-chr21:45340700..45342794,3	K562	blood:

Variant related genes	Relation type
AGPAT3	TF binding region
RNU6-859P	TF binding region
ENSG00000160213	Chromatin interaction
ENSG00000160216	Chromatin interaction
ENSG00000215458	Chromatin interaction
ENSG00000226543	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1005192	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13052200	0.81[ASN][1000 genomes]
rs1573474	0.81[ASN][1000 genomes]
rs1888525	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070547	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2186929	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838436	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838439	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3827246	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819340	0.92[EUR][1000 genomes]
rs4819345	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4819348	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819350	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6518334	0.85[EUR][1000 genomes]
rs6518335	0.90[EUR][1000 genomes]
rs6518337	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6518338	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7275972	0.81[ASN][1000 genomes]
rs7276578	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762404	0.81[ASN][1000 genomes]
rs8127341	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8133789	0.81[ASN][1000 genomes]
rs914196	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9306164	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9306165	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9306166	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9974282	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9978688	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9985035	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs999519	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1066284	chr21:45249549-45343314	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45336000-45344400	Enhancers	Liver	Liver
2	chr21:45336400-45351600	Weak transcription	Fetal Brain Female	brain
3	chr21:45337000-45342000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr21:45337200-45342400	Weak transcription	Colon Smooth Muscle	Colon
5	chr21:45337200-45350800	Weak transcription	Fetal Brain Male	brain
6	chr21:45337400-45342200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr21:45337400-45342200	Weak transcription	Brain Hippocampus Middle	brain
8	chr21:45337400-45342200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr21:45337400-45343200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr21:45337400-45344400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr21:45337600-45342000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr21:45337600-45342200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr21:45337600-45342600	Weak transcription	Brain Substantia Nigra	brain
14	chr21:45337600-45343200	Weak transcription	NHEK	skin
15	chr21:45337600-45344200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr21:45337600-45344400	Weak transcription	Dnd41	blood
17	chr21:45337600-45358600	Weak transcription	Osteobl	bone
18	chr21:45338200-45343200	Weak transcription	HSMM	muscle
19	chr21:45338800-45342200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr21:45338800-45342200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr21:45338800-45358600	Weak transcription	Hela-S3	cervix
22	chr21:45339600-45342000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:45339600-45342600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr21:45339600-45342600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr21:45339600-45342600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr21:45339600-45342800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr21:45339600-45344000	Enhancers	Gastric	stomach
28	chr21:45339600-45344400	Enhancers	Fetal Intestine Large	intestine
29	chr21:45339800-45342600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr21:45339800-45343800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr21:45339800-45346400	Enhancers	Right Ventricle	heart
32	chr21:45340000-45342200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr21:45340000-45342400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr21:45340000-45342600	Enhancers	Primary B cells from peripheral blood	blood
35	chr21:45340000-45343200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr21:45340000-45343800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr21:45340000-45344000	Enhancers	Fetal Muscle Leg	muscle
38	chr21:45340000-45344800	Enhancers	Fetal Muscle Trunk	muscle
39	chr21:45340000-45346400	Enhancers	Adipose Nuclei	Adipose
40	chr21:45340200-45342200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr21:45340200-45342200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr21:45340200-45342400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr21:45340200-45343800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr21:45340400-45342000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr21:45340400-45342200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr21:45340400-45342200	Weak transcription	Brain Angular Gyrus	brain
47	chr21:45340400-45342200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr21:45340400-45343600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr21:45340400-45344200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr21:45340600-45343600	Enhancers	Fetal Thymus	thymus

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