Variant report

Variant	rs3788152
Chromosome Location	chr21:46496122-46496123
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr21:46495384-46496715	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr21:46492353-46497285	IMR90	lung:	n/a	n/a
3	POLR2A	chr21:46496091-46496592	Hela-S3	cervix:	n/a	n/a
4	SMC3	chr21:46496049-46496624	Hela-S3	cervix:	n/a	n/a
5	TBP	chr21:46495519-46496749	Hela-S3	cervix:	n/a	n/a
6	CHD1	chr21:46493137-46497321	IMR90	lung:	n/a	n/a
7	MAFK	chr21:46496083-46496646	Hela-S3	cervix:	n/a	chr21:46496479-46496494 chr21:46496480-46496491
8	KAP1	chr21:46495094-46496570	HEK293	kidney:	n/a	n/a
9	POLR2A	chr21:46496090-46496483	Hela-S3	cervix:	n/a	n/a

No data

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65663723..65666241-chr21:46495274..46498090,2	K562	blood:
2	chr21:46495151..46497006-chr21:46906877..46909626,2	K562	blood:
3	chr21:46494891..46496808-chr21:46543893..46546977,3	K562	blood:
4	chr21:46494888..46496545-chr21:46914062..46916067,2	K562	blood:
5	chr21:46231513..46241255-chr21:46492035..46497390,26	K562	blood:
6	chr21:46348854..46378176-chr21:46489799..46500436,75	K562	blood:
7	chr21:46363747..46379047-chr21:46484156..46498795,67	K562	blood:
8	chr21:46492248..46501057-chr21:46545477..46562980,48	K562	blood:
9	chr21:46220974..46223825-chr21:46494380..46498218,5	MCF-7	breast:
10	chr21:46231904..46241990-chr21:46492035..46500735,28	K562	blood:
11	chr21:46495902..46496885-chr21:46556392..46557286,2	K562	blood:
12	chr21:46355061..46362857-chr21:46490375..46496482,13	K562	blood:
13	chr21:46493210..46496355-chr21:46960101..46962644,7	K562	blood:
14	chr21:46494805..46496748-chr21:46849949..46852672,3	K562	blood:
15	chr21:46494831..46496533-chr21:46576092..46578670,2	K562	blood:
16	chr21:46492507..46498258-chr21:46706665..46711571,8	K562	blood:
17	chr21:46420509..46434696-chr21:46492036..46497081,20	K562	blood:
18	chr21:46382465..46395146-chr21:46491921..46496809,22	K562	blood:
19	chr21:46387463..46395588-chr21:46492597..46498092,12	K562	blood:
20	chr21:46495879..46498410-chr21:46645680..46647627,2	K562	blood:
21	chr21:46492924..46497122-chr21:46547379..46551295,4	MCF-7	breast:
22	chr21:45553290..45555675-chr21:46493657..46496135,2	K562	blood:
23	chr21:46495410..46497788-chr21:46536429..46538983,2	K562	blood:
24	chr21:46390745..46393297-chr21:46494598..46497120,2	MCF-7	breast:
25	chr21:46494890..46496733-chr21:46901945..46904600,2	K562	blood:
26	chr21:46422255..46425486-chr21:46493644..46496852,6	K562	blood:
27	chr21:46494846..46497722-chr21:46974690..46977147,2	K562	blood:
28	chr21:46494154..46496164-chr21:46707875..46710753,3	K562	blood:
29	chr21:46494313..46497302-chr21:46514232..46516454,3	MCF-7	breast:
30	chr21:46398654..46417262-chr21:46491498..46498908,48	K562	blood:
31	chr21:46348334..46352514-chr21:46492914..46497675,5	K562	blood:
32	chr21:46495351..46497648-chr21:46516468..46519256,2	MCF-7	breast:
33	chr21:46491911..46497737-chr21:46547142..46552694,13	K562	blood:
34	chr21:46413441..46419649-chr21:46493522..46496485,6	K562	blood:
35	chr21:46493052..46496413-chr21:46547928..46550318,5	MCF-7	breast:
36	chr21:46493097..46497182-chr21:46538705..46543454,4	MCF-7	breast:
37	chr21:46493459..46496695-chr21:46925543..46928917,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268856	TF binding region
SSR4P1	TF binding region
ENSG00000261706	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000182871	Chromatin interaction
ENSG00000234880	Chromatin interaction
ENSG00000224930	Chromatin interaction
ENSG00000186866	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000272825	Chromatin interaction
ENSG00000268805	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000160221	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000215447	Chromatin interaction
ENSG00000173638	Chromatin interaction
ENSG00000184900	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17004733	0.92[CEU][hapmap]
rs387097	0.92[CEU][hapmap]
rs7275998	0.89[CEU][hapmap]
rs729895	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs73907241	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs872768	0.92[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv834110	chr21:46316183-46505151	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
3	esv3355416	chr21:46492024-46497122	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3788152	SSR4P1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46493600-46496200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:46493600-46496600	Active TSS	HSMM	muscle
3	chr21:46493600-46496800	Active TSS	Aorta	Aorta
4	chr21:46493800-46496200	Active TSS	HSMMtube	muscle
5	chr21:46495000-46496200	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr21:46495000-46496600	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr21:46495000-46496600	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr21:46495200-46496200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr21:46495200-46496400	Flanking Active TSS	Primary B cells from peripheral blood	blood
10	chr21:46495200-46496400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr21:46495200-46496400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr21:46495200-46496600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr21:46495200-46496600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:46495200-46496600	Flanking Active TSS	K562	blood
15	chr21:46495400-46496200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr21:46495400-46496200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr21:46495400-46496200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr21:46495400-46496200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr21:46495400-46496400	Flanking Active TSS	HepG2	liver
20	chr21:46495400-46496600	Flanking Active TSS	HUVEC	blood vessel
21	chr21:46495400-46496600	Flanking Active TSS	NHEK	skin
22	chr21:46495400-46496600	Flanking Active TSS	Osteobl	bone
23	chr21:46495400-46497000	Enhancers	Fetal Heart	heart
24	chr21:46495400-46497200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr21:46495600-46496200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
26	chr21:46495600-46496200	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr21:46495600-46496200	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr21:46495600-46496200	Active TSS	Fetal Muscle Trunk	muscle
29	chr21:46495600-46496200	Active TSS	Right Atrium	heart
30	chr21:46495600-46496200	Active TSS	Right Ventricle	heart
31	chr21:46495600-46496400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr21:46495600-46496400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr21:46495600-46496400	Active TSS	Lung	lung
34	chr21:46495600-46496400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
35	chr21:46495600-46496400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
36	chr21:46495600-46496400	Enhancers	Small Intestine	intestine
37	chr21:46495600-46496400	Enhancers	Spleen	Spleen
38	chr21:46495600-46496600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr21:46495600-46496600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr21:46495600-46496800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr21:46495600-46497000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr21:46495600-46497000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr21:46495600-46500200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr21:46495600-46501400	Weak transcription	Gastric	stomach
45	chr21:46495800-46496200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr21:46495800-46496200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr21:46495800-46496200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
48	chr21:46495800-46496200	Active TSS	Brain Anterior Caudate	brain
49	chr21:46495800-46496200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
50	chr21:46495800-46496200	Active TSS	Brain Hippocampus Middle	brain

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