Variant report

Variant	rs139888239
Chromosome Location	chr21:40720262-40720263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:161)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:161 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr21:40716967-40721099	SK-N-SH	brain:	n/a	n/a
2	YY1	chr21:40719940-40721055	GM12878	blood:	n/a	n/a
3	HEY1	chr21:40720124-40721066	K562	blood:	n/a	n/a
4	POLR2A	chr21:40720133-40720548	GM12891	blood:	n/a	n/a
5	ZKSCAN1	chr21:40720233-40720425	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr21:40720171-40722416	GM12878	blood:	n/a	n/a
7	POLR2A	chr21:40720101-40721055	Hela-S3	cervix:	n/a	n/a
8	YY1	chr21:40720099-40720741	HepG2	liver:	n/a	n/a
9	POLR2A	chr21:40720026-40721115	GM12892	blood:	n/a	n/a
10	POLR2A	chr21:40720101-40723328	K562	blood:	n/a	n/a
11	RCOR1	chr21:40720153-40720655	K562	blood:	n/a	n/a
12	POLR2A	chr21:40719451-40723014	GM12878	blood:	n/a	n/a
13	MTA3	chr21:40720046-40720607	GM12878	blood:	n/a	n/a
14	MXI1	chr21:40720262-40720267	Hela-S3	cervix:	n/a	n/a
15	REST	chr21:40719476-40722011	H1-neurons	neurons:	n/a	chr21:40721572-40721585 chr21:40721572-40721585
16	POLR2A	chr21:40716164-40723345	K562	blood:	n/a	n/a
17	YY1	chr21:40720063-40720303	A549	lung:	n/a	n/a
18	TAF1	chr21:40720100-40721872	ECC-1	luminal epithelium:	n/a	n/a
19	E2F4	chr21:40719770-40721703	MCF10A-Er-Src	breast:	n/a	chr21:40720601-40720612 chr21:40721328-40721337 chr21:40721584-40721593 chr21:40721170-40721179
20	SIN3AK20	chr21:40719291-40722472	MCF-7	breast:	n/a	n/a
21	ZNF143	chr21:40720184-40720366	Hela-S3	cervix:	n/a	n/a
22	MXI1	chr21:40719317-40721951	IMR90	lung:	n/a	n/a
23	POLR2A	chr21:40719983-40722069	GM12878	blood:	n/a	n/a
24	POLR2A	chr21:40720245-40721551	IMR90	lung:	n/a	n/a
25	POLR2A	chr21:40720147-40721849	Hela-S3	cervix:	n/a	n/a
26	SIN3AK20	chr21:40720092-40721055	PANC-1	pancreas:	n/a	n/a
27	YY1	chr21:40720035-40721147	GM12878	blood:	n/a	n/a
28	ETS1	chr21:40720192-40721055	K562	blood:	n/a	n/a
29	POLR2A	chr21:40720076-40721155	HL-60	blood:	n/a	n/a
30	POLR2A	chr21:40720190-40721112	K562	blood:	n/a	n/a
31	YY1	chr21:40720058-40721093	GM12892	blood:	n/a	n/a
32	TAF1	chr21:40720098-40721068	H1-hESC	embryonic stem cell:	n/a	n/a
33	SIN3A	chr21:40720084-40720603	GM12878	blood:	n/a	n/a
34	POLR2A	chr21:40720254-40721256	Gliobla	brain:	n/a	n/a
35	CHD2	chr21:40720173-40721958	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr21:40720156-40720768	U87	brain:	n/a	n/a
37	TAF1	chr21:40720110-40721148	H1-neurons	neurons:	n/a	n/a
38	MAZ	chr21:40720109-40721772	IMR90	lung:	n/a	n/a
39	HEY1	chr21:40720136-40721048	K562	blood:	n/a	n/a
40	MYC	chr21:40719529-40722622	K562	blood:	n/a	n/a
41	MAFK	chr21:40720245-40720329	HepG2	liver:	n/a	n/a
42	POLR2A	chr21:40720095-40722140	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr21:40719978-40721123	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr21:40720211-40721094	HL-60	blood:	n/a	n/a
45	POLR2A	chr21:40719377-40722068	H1-hESC	embryonic stem cell:	n/a	n/a
46	CHD1	chr21:40719934-40720638	GM12878	blood:	n/a	n/a
47	POLR2A	chr21:40720040-40720745	GM12892	blood:	n/a	n/a
48	POLR2A	chr21:40720156-40722146	MCF10A-Er-Src	breast:	n/a	n/a
49	ZNF143	chr21:40720146-40720519	H1-hESC	embryonic stem cell:	n/a	n/a
50	E2F4	chr21:40720239-40721922	K562	blood:	n/a	chr21:40720601-40720612 chr21:40721328-40721337 chr21:40721584-40721593 chr21:40721170-40721179

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24607940..24610732-chr21:40718347..40720759,2	MCF-7	breast:
2	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
3	chr20:49347681..49350459-chr21:40719549..40721947,2	MCF-7	breast:
4	chr21:40685861..40686376-chr21:40719745..40720551,2	MCF-7	breast:
5	chr21:40718950..40720909-chr8:144820152..144822605,2	MCF-7	breast:
6	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
7	chr21:40716662..40723444-chr21:40748337..40754328,16	MCF-7	breast:
8	chr21:40635414..40638745-chr21:40717382..40720310,3	K562	blood:
9	chr21:40719359..40724848-chr21:40748806..40754741,7	MCF-7	breast:
10	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
11	chr21:40650313..40652723-chr21:40719146..40721312,2	MCF-7	breast:
12	chr21:40719979..40722729-chr21:40816056..40819504,5	MCF-7	breast:
13	chr21:40719750..40724652-chr21:40748317..40754270,9	K562	blood:
14	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
15	chr21:40553821..40557385-chr21:40719764..40724370,6	K562	blood:
16	chr21:40719238..40723494-chr21:40813785..40819496,7	MCF-7	breast:
17	chr21:40716961..40722807-chr21:40750720..40754894,10	K562	blood:
18	chr12:57893868..57894739-chr21:40720155..40721007,2	MCF-7	breast:
19	chr21:40719170..40722188-chr21:40780437..40783108,3	MCF-7	breast:
20	chr21:40719410..40723060-chr21:40814028..40819084,9	K562	blood:
21	chr21:40719273..40720815-chr21:40782667..40784260,2	K562	blood:
22	chr21:40554663..40558370-chr21:40719503..40722190,4	MCF-7	breast:
23	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238556	TF binding region
HMGN1	TF binding region
ENSG00000185437	Chromatin interaction
ENSG00000259321	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000157578	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv3439352	chr21:40719607-40722455	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40717000-40720400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr21:40717400-40720400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
3	chr21:40717600-40720400	Transcr. at gene 5' and 3'	A549	lung
4	chr21:40717600-40720400	Transcr. at gene 5' and 3'	K562	blood
5	chr21:40718000-40721400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr21:40718200-40720400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr21:40718400-40720400	Active TSS	Right Atrium	heart
8	chr21:40718800-40720400	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr21:40718800-40721400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr21:40718800-40721600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr21:40718800-40721600	Active TSS	Brain Germinal Matrix	brain
12	chr21:40718800-40721600	Active TSS	Fetal Stomach	stomach
13	chr21:40718800-40721800	Active TSS	Fetal Intestine Large	intestine
14	chr21:40718800-40721800	Active TSS	Fetal Intestine Small	intestine
15	chr21:40718800-40722000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr21:40718800-40722200	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr21:40718800-40722200	Active TSS	GM12878-XiMat	blood
18	chr21:40719000-40720400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr21:40719000-40721600	Active TSS	HMEC	breast
20	chr21:40719000-40722200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr21:40719000-40722400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr21:40719200-40720400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr21:40719200-40722000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr21:40719200-40722000	Active TSS	Fetal Brain Female	brain
25	chr21:40719200-40722000	Active TSS	HSMM	muscle
26	chr21:40719200-40722000	Active TSS	HSMMtube	muscle
27	chr21:40719200-40722200	Active TSS	Fetal Kidney	kidney
28	chr21:40719200-40722400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr21:40719200-40722800	Active TSS	Hela-S3	cervix
30	chr21:40719400-40720400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr21:40719400-40721400	Active TSS	Primary T cells fromperipheralblood	blood
32	chr21:40719400-40721600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr21:40719400-40721600	Active TSS	Fetal Muscle Trunk	muscle
34	chr21:40719400-40721800	Active TSS	Ovary	ovary
35	chr21:40719400-40721800	Active TSS	Right Ventricle	heart
36	chr21:40719400-40722000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr21:40719400-40722200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr21:40719400-40722200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr21:40719400-40722400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr21:40719400-40722600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr21:40719600-40720400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr21:40719600-40720400	ZNF genes & repeats	Fetal Brain Male	brain
43	chr21:40719600-40720600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr21:40719600-40720600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr21:40719600-40720600	Active TSS	Fetal Heart	heart
46	chr21:40719600-40720600	Active TSS	Stomach Mucosa	stomach
47	chr21:40719600-40721600	Active TSS	Colonic Mucosa	Colon
48	chr21:40719600-40721600	Active TSS	Placenta	Placenta
49	chr21:40719600-40721600	Active TSS	Thymus	Thymus
50	chr21:40719600-40721800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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