Variant report

Variant	rs2735307
Chromosome Location	chr21:40713358-40713359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40713112-40713610	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr21:40713164-40713521	GM12878	blood:	n/a	n/a
3	PML	chr21:40712739-40714047	K562	blood:	n/a	n/a
4	POLR2A	chr21:40712648-40714047	HepG2	liver:	n/a	n/a
5	POLR2A	chr21:40712320-40713908	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:40712533-40714043	GM12892	blood:	n/a	n/a
7	POLR2A	chr21:40712664-40714026	GM12878	blood:	n/a	n/a
8	POLR2A	chr21:40712540-40713998	GM12891	blood:	n/a	n/a
9	POLR2A	chr21:40712283-40714096	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr21:40712609-40714043	K562	blood:	n/a	n/a
11	POLR2A	chr21:40712665-40714086	GM19193	blood:	n/a	n/a
12	POLR2A	chr21:40712936-40713979	H1-hESC	embryonic stem cell:	n/a	n/a
13	PML	chr21:40713221-40713973	K562	blood:	n/a	n/a
14	POLR2A	chr21:40713324-40713476	GM12878	blood:	n/a	n/a
15	POLR2A	chr21:40712648-40714029	GM12891	blood:	n/a	n/a
16	POLR2A	chr21:40712617-40713847	HepG2	liver:	n/a	n/a
17	POLR2A	chr21:40713055-40713824	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr21:40713113-40713870	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr21:40712691-40714288	K562	blood:	n/a	n/a
20	POLR2A	chr21:40712641-40713984	K562	blood:	n/a	n/a
21	POLR2A	chr21:40712655-40713946	HepG2	liver:	n/a	n/a
22	POLR2A	chr21:40712599-40714102	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr21:40713118-40714174	K562	blood:	n/a	n/a
24	POLR2A	chr21:40712660-40713861	HEK293	kidney:	n/a	n/a
25	POLR2A	chr21:40712480-40713812	GM12892	blood:	n/a	n/a
26	POLR2A	chr21:40713179-40713520	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr21:40712618-40713861	PBDE	blood:	n/a	n/a
28	POLR2A	chr21:40713156-40713528	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr21:40712684-40713993	GM12891	blood:	n/a	n/a
30	POLR2A	chr21:40711172-40713994	MCF-7	breast:	n/a	n/a
31	POLR2A	chr21:40713065-40713959	GM12891	blood:	n/a	n/a
32	POLR2A	chr21:40713222-40713496	GM12878	blood:	n/a	n/a
33	POLR2A	chr21:40712500-40713580	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr21:40712881-40714032	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr21:40712445-40714030	HL-60	blood:	n/a	n/a
36	POLR2A	chr21:40712563-40714113	GM12892	blood:	n/a	n/a
37	POLR2A	chr21:40712641-40713800	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr21:40713116-40713888	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr21:40711343-40714219	K562	blood:	n/a	n/a
40	POLR2A	chr21:40712946-40714030	U87	brain:	n/a	n/a
41	POLR2A	chr21:40712234-40713900	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr21:40712249-40714148	GM12878	blood:	n/a	n/a
43	POU2F2	chr21:40713156-40713546	GM12891	blood:	n/a	n/a
44	POLR2A	chr21:40712654-40714049	GM12892	blood:	n/a	n/a
45	POLR2A	chr21:40713295-40713920	HCT-116	colon:	n/a	n/a
46	POLR2A	chr21:40712533-40713460	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr21:40712494-40714132	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr21:40712706-40714014	GM12892	blood:	n/a	n/a
49	POLR2A	chr21:40713075-40713945	U87	brain:	n/a	n/a
50	POLR2A	chr21:40712468-40713820	SK-N-SH	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	21:40712819-40717370..21:40748850-40752541	GM12878	blood:
2	chr21:40691885..40693506-chr21:40712326..40714444,2	K562	blood:
3	chr21:40681057..40687929-chr21:40707012..40715318,11	K562	blood:
4	chr21:40646616..40649505-chr21:40712893..40714626,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000252915	TF binding region
ENSG00000182093	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000238141	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2249666	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2735308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2776306	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776312	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2854727	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2989329	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3167757	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs741795	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8128901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8128919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129303	0.90[AFR][1000 genomes]
rs8132993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914156	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980890	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[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	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	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2735307	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2735307	HMGN1	cis	multi-tissue	Pritchard
rs2735307	PSMG1	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40692400-40718400	Weak transcription	Right Atrium	heart
2	chr21:40704000-40719600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:40704400-40713400	Weak transcription	Hela-S3	cervix
4	chr21:40704400-40715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr21:40704400-40715200	Weak transcription	Spleen	Spleen
6	chr21:40704600-40713800	Weak transcription	Ovary	ovary
7	chr21:40704600-40717200	Weak transcription	Right Ventricle	heart
8	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr21:40704800-40715200	Weak transcription	Fetal Heart	heart
10	chr21:40708800-40713400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr21:40708800-40715200	Weak transcription	Gastric	stomach
12	chr21:40709000-40713400	Weak transcription	Stomach Mucosa	stomach
13	chr21:40710000-40715200	Weak transcription	Small Intestine	intestine
14	chr21:40710400-40713600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr21:40710400-40715400	Weak transcription	Psoas Muscle	Psoas
16	chr21:40711200-40713400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr21:40711400-40713600	Weak transcription	Brain Hippocampus Middle	brain
18	chr21:40711400-40714200	Weak transcription	Brain Angular Gyrus	brain
19	chr21:40711600-40713400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr21:40711600-40713400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr21:40711600-40713400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr21:40711600-40713600	Weak transcription	NHDF-Ad	bronchial
23	chr21:40711600-40715400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr21:40711800-40713400	Weak transcription	Brain Anterior Caudate	brain
25	chr21:40711800-40715000	Weak transcription	NHLF	lung
26	chr21:40711800-40715200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:40711800-40715200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr21:40711800-40715200	Weak transcription	Brain Substantia Nigra	brain
29	chr21:40711800-40719600	Weak transcription	Pancreas	Pancrea
30	chr21:40712000-40715200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr21:40712000-40715200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr21:40712000-40715200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr21:40712000-40715200	Weak transcription	Aorta	Aorta
34	chr21:40712000-40717200	Strong transcription	Fetal Stomach	stomach
35	chr21:40712200-40716000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr21:40712200-40716200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr21:40712200-40718800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr21:40712400-40715800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr21:40712600-40714200	Strong transcription	Primary T cells from cord blood	blood
40	chr21:40712600-40714200	Strong transcription	Brain Cingulate Gyrus	brain
41	chr21:40712600-40714200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr21:40712600-40715200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr21:40712600-40715400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr21:40712600-40716000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr21:40712600-40716400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr21:40712600-40716600	Strong transcription	Fetal Brain Female	brain
47	chr21:40712600-40716800	Strong transcription	Dnd41	blood
48	chr21:40712600-40717000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr21:40712600-40717000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr21:40712600-40717000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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