Variant report

Variant	rs35123057
Chromosome Location	chr21:40711689-40711690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40711666-40711726	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr21:40711014-40712473	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr21:40711172-40713994	MCF-7	breast:	n/a	n/a
4	POLR2A	chr21:40711343-40714219	K562	blood:	n/a	n/a
5	CEBPB	chr21:40711631-40711790	HepG2	liver:	n/a	n/a
6	POLR2A	chr21:40711621-40711792	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr21:40711338-40711759	GM12878	blood:	n/a	n/a
8	POLR2A	chr21:40711636-40711690	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	21:40553066-40557191..21:40702099-40712819	K562	blood:
2	chr21:40681057..40687929-chr21:40707012..40715318,11	K562	blood:
3	chr21:40696329..40702419-chr21:40706472..40712889,11	K562	blood:
4	21:40702099-40712819..21:40757151-40764378	K562	blood:

No data

Variant related genes	Relation type
ENSG00000252915	TF binding region
ENSG00000183527	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000238141	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1041440	0.87[AMR][1000 genomes]
rs10427502	0.84[AMR][1000 genomes]
rs12151994	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13047663	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13047678	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13625	0.89[AMR][1000 genomes]
rs1541102	0.84[AMR][1000 genomes]
rs1963676	0.92[AFR][1000 genomes]
rs2026267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150415	0.87[AMR][1000 genomes]
rs2249651	0.90[ASN][1000 genomes]
rs2735306	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360661	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836938	0.81[AMR][1000 genomes]
rs2836953	0.86[AMR][1000 genomes]
rs2836957	0.87[AMR][1000 genomes]
rs2836964	0.84[AMR][1000 genomes]
rs2836965	0.87[AMR][1000 genomes]
rs2836967	0.90[AMR][1000 genomes]
rs2836968	0.87[AMR][1000 genomes]
rs2836972	0.87[AMR][1000 genomes]
rs2836973	0.86[AMR][1000 genomes]
rs2836974	0.90[AMR][1000 genomes]
rs2836977	0.89[AMR][1000 genomes]
rs2989330	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433511	0.86[AMR][1000 genomes]
rs34578707	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34672724	0.91[AMR][1000 genomes]
rs35068861	0.90[AMR][1000 genomes]
rs35560196	0.91[AMR][1000 genomes]
rs55836299	0.86[AMR][1000 genomes]
rs56306759	0.84[AMR][1000 genomes]
rs6517533	0.87[AMR][1000 genomes]
rs6517538	0.90[AMR][1000 genomes]
rs68004583	0.87[AMR][1000 genomes]
rs7277978	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7282624	0.89[AMR][1000 genomes]
rs7283420	0.81[AMR][1000 genomes]
rs7283516	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7283569	0.87[AMR][1000 genomes]
rs7354783	0.87[AMR][1000 genomes]
rs8128102	0.82[AMR][1000 genomes]
rs8128620	0.89[AMR][1000 genomes]
rs8128827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128894	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8129147	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8129303	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129416	0.87[AMR][1000 genomes]
rs8130984	0.90[AMR][1000 genomes]
rs8131965	0.80[AMR][1000 genomes]
rs8133146	0.87[AMR][1000 genomes]
rs8134733	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs914156	0.82[AFR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35123057	HMGN1	cis	multi-tissue	Pritchard
rs35123057	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs35123057	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs35123057	PSMG1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:113 , 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	chr21:40699200-40712600	Weak transcription	Fetal Muscle Leg	muscle
3	chr21:40704000-40719600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr21:40704200-40712800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr21:40704200-40712800	Weak transcription	A549	lung
6	chr21:40704200-40713200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr21:40704400-40712200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr21:40704400-40712600	Weak transcription	Fetal Intestine Large	intestine
9	chr21:40704400-40712800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr21:40704400-40713000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr21:40704400-40713000	Weak transcription	Fetal Intestine Small	intestine
12	chr21:40704400-40713200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr21:40704400-40713400	Weak transcription	Hela-S3	cervix
14	chr21:40704400-40715000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr21:40704400-40715200	Weak transcription	Spleen	Spleen
16	chr21:40704600-40712600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:40704600-40712600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr21:40704600-40712600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr21:40704600-40712600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr21:40704600-40712800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr21:40704600-40712800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:40704600-40712800	Weak transcription	Left Ventricle	heart
23	chr21:40704600-40712800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr21:40704600-40713200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr21:40704600-40713200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr21:40704600-40713800	Weak transcription	Ovary	ovary
27	chr21:40704600-40717200	Weak transcription	Right Ventricle	heart
28	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr21:40704800-40712800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr21:40704800-40715200	Weak transcription	Fetal Heart	heart
31	chr21:40705000-40713000	Weak transcription	K562	blood
32	chr21:40705400-40712600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr21:40708600-40712600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:40708600-40712800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr21:40708600-40712800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr21:40708800-40712600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr21:40708800-40712600	Weak transcription	Thymus	Thymus
38	chr21:40708800-40712600	Weak transcription	Osteobl	bone
39	chr21:40708800-40712800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr21:40708800-40712800	Weak transcription	Placenta	Placenta
41	chr21:40708800-40713000	Weak transcription	Esophagus	oesophagus
42	chr21:40708800-40713200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr21:40708800-40713400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr21:40708800-40715200	Weak transcription	Gastric	stomach
45	chr21:40709000-40713400	Weak transcription	Stomach Mucosa	stomach
46	chr21:40709400-40712800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr21:40709600-40712800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr21:40709600-40713200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr21:40709800-40712600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr21:40710000-40715200	Weak transcription	Small Intestine	intestine

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