Variant report

Variant	rs428428
Chromosome Location	chr21:46219184-46219185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr21:46218910-46219218	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr21:46217908-46219811	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:46219184-46219234	K562	blood:	n/a
2	chr21:46219184-46219234	NT2-D1	testis:	n/a
3	chr21:46219184-46219234	PrEC	prostate:	n/a
4	chr21:46219184-46219234	HMEC	breast:	n/a
5	chr21:46219184-46219234	BE2_C	brain:	n/a
6	chr21:46219184-46219234	MCF10A-Er-Src	breast:	n/a
7	chr21:46219184-46219234	MCF-7	breast:	n/a
8	chr21:46219184-46219234	SAEC	small airway:	n/a
9	chr21:46219184-46219234	HRCEpiC	kidney:	n/a
10	chr21:46219184-46219234	NB4	blood:	n/a
11	chr21:46219184-46219234	BJ	skin:	n/a
12	chr21:46219184-46219234	HCM	heart:	n/a
13	chr21:46219184-46219234	AG09309	skin:	n/a
14	chr21:46219184-46219234	SK-N-SH_RA	brain:	n/a
15	chr21:46219184-46219234	AoSMC	blood vessel:	n/a
16	chr21:46219184-46219234	GM12891	blood:	n/a
17	chr21:46219184-46219234	NH-A	brain:	n/a
18	chr21:46219184-46219234	PFSK-1	brain:	n/a
19	chr21:46219184-46219234	U87	brain:	n/a
20	chr21:46219184-46219234	RPTEC	kidney:	n/a
21	chr21:46219184-46219234	HRPEpiC	eye:	n/a
22	chr21:46219184-46219234	SK-N-SH	brain:	n/a
23	chr21:46219184-46219234	GM19239	blood:	n/a
24	chr21:46219184-46219234	PANC-1	pancreas:	n/a
25	chr21:46219184-46219234	HRE	kidney:	n/a
26	chr21:46219184-46219234	LNCaP	prostate:	n/a
27	chr21:46219184-46219234	HEK293	kidney:	embryo
28	chr21:46219184-46219234	HUVEC	blood vessel:	n/a
29	chr21:46219184-46219234	AG04450	lung:	fetal
30	chr21:46219184-46219234	NHBE	bronchial:	n/a
31	chr21:46219184-46219234	CMK	blood:	n/a
32	chr21:46219184-46219234	AG10803	skin:	n/a
33	chr21:46219184-46219234	HEEpiC	esophagus:	n/a
34	chr21:46219184-46219234	NHDF-neo	bronchial:	n/a
35	chr21:46219184-46219234	HAEpiC	amniotic membrane:	n/a
36	chr21:46219184-46219234	HepG2	liver:	n/a
37	chr21:46219184-46219234	AG09319	gingival:	n/a
38	chr21:46219184-46219234	HCF	heart:	n/a
39	chr21:46219184-46219234	T-47D	breast:	n/a
40	chr21:46219184-46219234	Hela-S3	cervix:	n/a
41	chr21:46219184-46219234	GM06990	blood:	n/a
42	chr21:46219184-46219234	Caco-2	colon:	n/a
43	chr21:46219184-46219234	HPAEpiC	pulmonary alveolar:	n/a
44	chr21:46219184-46219234	HCT-116	colon:	n/a
45	chr21:46219184-46219234	SKMC	muscle:	n/a
46	chr21:46219184-46219234	A549	lung:	n/a
47	chr21:46219184-46219234	HCPEpiC	choroid plexus:	n/a
48	chr21:46219184-46219234	GM12878	blood:	n/a
49	chr21:46219184-46219234	H1-hESC	embryonic stem cell:	embryo
50	chr21:46219184-46219234	HIPEpiC	eye:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46218606..46224662-chr21:46357422..46363606,13	MCF-7	breast:
2	chr21:46218558..46223428-chr21:46289542..46296056,15	MCF-7	breast:
3	chr21:46218586..46220158-chr21:46274953..46276818,2	K562	blood:
4	chr21:46218496..46222154-chr21:46279503..46283710,3	MCF-7	breast:
5	chr21:46213336..46214943-chr21:46217277..46219676,2	MCF-7	breast:
6	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
7	chr21:46216948..46220007-chr21:46331452..46334687,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236519	TF binding region
ENSG00000236519	CpG island
ENSG00000160255	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000160256	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1141	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217834	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17289578	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17289745	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017089	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838681	1.00[ASN][1000 genomes]
rs2838683	1.00[ASN][1000 genomes]
rs2838689	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28728356	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73232950	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873301	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977684	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46189000-46221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:46195000-46219800	Weak transcription	Small Intestine	intestine
3	chr21:46195400-46220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:46197200-46220400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr21:46198800-46219600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr21:46198800-46220000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr21:46198800-46220000	Weak transcription	Fetal Kidney	kidney
8	chr21:46200000-46220400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr21:46201200-46220400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr21:46202400-46219200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr21:46203400-46220000	Weak transcription	Fetal Brain Female	brain
12	chr21:46205200-46220400	Weak transcription	Aorta	Aorta
13	chr21:46205200-46220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr21:46206200-46219800	Weak transcription	Right Ventricle	heart
15	chr21:46206200-46220000	Weak transcription	Brain Germinal Matrix	brain
16	chr21:46206400-46220000	Weak transcription	Brain Hippocampus Middle	brain
17	chr21:46206800-46220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr21:46210000-46220000	Weak transcription	Fetal Brain Male	brain
19	chr21:46210200-46220000	Weak transcription	NH-A	brain
20	chr21:46211600-46220400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr21:46211800-46220400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr21:46212000-46220000	Weak transcription	Lung	lung
23	chr21:46212000-46220400	Weak transcription	Colonic Mucosa	Colon
24	chr21:46212400-46220400	Weak transcription	Spleen	Spleen
25	chr21:46212600-46219800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr21:46213400-46219400	Weak transcription	Colon Smooth Muscle	Colon
27	chr21:46213400-46219400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr21:46213400-46219600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr21:46213400-46219600	Weak transcription	Psoas Muscle	Psoas
30	chr21:46213400-46219800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr21:46213400-46219800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr21:46213400-46219800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr21:46213400-46219800	Weak transcription	Brain Substantia Nigra	brain
34	chr21:46213400-46219800	Weak transcription	Fetal Heart	heart
35	chr21:46213400-46219800	Weak transcription	Pancreas	Pancrea
36	chr21:46213400-46219800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr21:46213400-46219800	Weak transcription	HSMMtube	muscle
38	chr21:46213400-46220000	Weak transcription	Esophagus	oesophagus
39	chr21:46213400-46220000	Weak transcription	Right Atrium	heart
40	chr21:46213400-46220200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr21:46213400-46220400	Weak transcription	Brain Angular Gyrus	brain
42	chr21:46214000-46219800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr21:46214000-46219800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr21:46214000-46219800	Weak transcription	NHDF-Ad	bronchial
45	chr21:46214200-46219600	Weak transcription	Fetal Intestine Small	intestine
46	chr21:46214200-46220400	Weak transcription	Gastric	stomach
47	chr21:46215400-46219400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr21:46215400-46219800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr21:46215400-46219800	Strong transcription	NHEK	skin
50	chr21:46215600-46219200	Strong transcription	Adipose Nuclei	Adipose

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