Variant report

Variant	rs2776312
Chromosome Location	chr21:40718518-40718519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40718431-40718920	GM12878	blood:	n/a	n/a
2	MXI1	chr21:40716967-40721099	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr21:40717311-40718928	GM12891	blood:	n/a	n/a
4	POLR2A	chr21:40716164-40723345	K562	blood:	n/a	n/a
5	IRF1	chr21:40718316-40720432	K562	blood:	n/a	n/a
6	E2F4	chr21:40718517-40718717	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr21:40718447-40719086	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr21:40718516-40718801	HepG2	liver:	n/a	n/a
9	POLR2A	chr21:40718415-40718922	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr21:40718445-40718791	HepG2	liver:	n/a	n/a
11	POLR2A	chr21:40718401-40718784	GM12878	blood:	n/a	n/a
12	MYC	chr21:40718135-40718667	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:14 , 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	21:40583765-40590917..21:40718004-40719183	GM12878	blood:
4	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
5	chr21:40716662..40723444-chr21:40748337..40754328,16	MCF-7	breast:
6	chr21:40635414..40638745-chr21:40717382..40720310,3	K562	blood:
7	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
8	21:40718004-40719183..21:40748850-40752541	GM12878	blood:
9	chr21:40555099..40556872-chr21:40718336..40720047,2	MCF-7	breast:
10	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
11	chr21:40652004..40654564-chr21:40716456..40719134,2	MCF-7	breast:
12	chr21:40716961..40722807-chr21:40750720..40754894,10	K562	blood:
13	21:40565363-40575691..21:40718004-40719183	GM12878	blood:
14	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:

No data

Variant related genes	Relation type
HMGN1	TF binding region
ENSG00000238556	TF binding region
ENSG00000232608	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000259321	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2249666	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2735307	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2735308	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2776306	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2776311	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2854727	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2989329	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3167757	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs741795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8128901	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8128919	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8132993	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs914156	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9980890	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2776312	HMGN1	cis	multi-tissue	Pritchard
rs2776312	HMGN1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40704000-40719600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40711800-40719600	Weak transcription	Pancreas	Pancrea
4	chr21:40712200-40718800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr21:40712800-40718600	Strong transcription	Primary B cells from peripheral blood	blood
6	chr21:40712800-40719200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr21:40712800-40719200	Strong transcription	Placenta	Placenta
8	chr21:40713000-40718800	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr21:40713600-40718600	Strong transcription	NHDF-Ad	bronchial
10	chr21:40715000-40719000	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr21:40715600-40719200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr21:40715800-40718600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr21:40715800-40718800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr21:40715800-40719400	Weak transcription	Ovary	ovary
15	chr21:40715800-40719600	Weak transcription	Esophagus	oesophagus
16	chr21:40716000-40718600	Weak transcription	Brain Angular Gyrus	brain
17	chr21:40716000-40718600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr21:40716000-40719400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr21:40716000-40719400	Weak transcription	Brain Anterior Caudate	brain
20	chr21:40716000-40719600	Weak transcription	Aorta	Aorta
21	chr21:40716000-40719600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr21:40716000-40719600	Weak transcription	Colonic Mucosa	Colon
23	chr21:40716000-40719600	Weak transcription	Gastric	stomach
24	chr21:40716000-40719600	Weak transcription	Lung	lung
25	chr21:40716000-40719600	Weak transcription	Psoas Muscle	Psoas
26	chr21:40716000-40719600	Weak transcription	Small Intestine	intestine
27	chr21:40716200-40718600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr21:40716200-40718600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr21:40716200-40720000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr21:40716400-40718600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr21:40716400-40719400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr21:40716400-40720000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr21:40716600-40719000	Genic enhancers	Primary T cells from cord blood	blood
34	chr21:40716600-40719200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr21:40716600-40719600	Weak transcription	Brain Substantia Nigra	brain
36	chr21:40716800-40719200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
37	chr21:40716800-40719800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr21:40717000-40718600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr21:40717000-40718800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr21:40717000-40718800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr21:40717000-40718800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr21:40717000-40718800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr21:40717000-40718800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
44	chr21:40717000-40719400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr21:40717000-40720400	Transcr. at gene 5' and 3'	Dnd41	blood
46	chr21:40717200-40718600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
47	chr21:40717200-40718600	Genic enhancers	HepG2	liver
48	chr21:40717200-40718800	Genic enhancers	Primary hematopoietic stem cells	blood
49	chr21:40717200-40719600	Weak transcription	Left Ventricle	heart
50	chr21:40717200-40719600	Transcr. at gene 5' and 3'	NH-A	brain

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