Variant report

Variant	rs2776309
Chromosome Location	chr21:40715791-40715792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40715120-40715980	GM12878	blood:	n/a	n/a
2	POLR2A	chr21:40714109-40716057	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr21:40715105-40715917	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
2	21:40712819-40717370..21:40748850-40752541	GM12878	blood:
3	chr21:40555173..40557304-chr21:40714737..40716613,2	K562	blood:

Variant related genes	Relation type
ENSG00000252915	TF binding region
ENSG00000238141	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1041440	0.87[AMR][1000 genomes]
rs10427502	0.84[AMR][1000 genomes]
rs12151994	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12482181	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs13047663	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13047678	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13049280	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13050927	0.83[CHD][hapmap]
rs13339986	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs13625	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[AMR][1000 genomes]
rs14194	0.86[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1541102	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes]
rs1571709	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs1963676	0.92[AFR][1000 genomes]
rs1984022	0.90[CEU][hapmap]
rs2026265	0.88[CEU][hapmap]
rs2026267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150415	0.91[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes]
rs2234543	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2249651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2410123	0.83[LWK][hapmap]
rs2735306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776311	0.86[YRI][hapmap]
rs28360661	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2836925	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2836928	1.00[JPT][hapmap]
rs2836929	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2836932	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2836933	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836938	0.81[AMR][1000 genomes]
rs2836939	0.81[MEX][hapmap]
rs2836953	0.86[AMR][1000 genomes]
rs2836955	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836957	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes]
rs2836964	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes]
rs2836965	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes]
rs2836967	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs2836968	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes]
rs2836972	0.87[AMR][1000 genomes]
rs2836973	0.86[AMR][1000 genomes]
rs2836974	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes]
rs2836977	0.89[AMR][1000 genomes]
rs2836987	0.83[LWK][hapmap]
rs2854727	0.93[ASW][hapmap];0.86[YRI][hapmap]
rs2989330	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433511	0.86[AMR][1000 genomes]
rs34578707	0.81[AMR][1000 genomes]
rs34672724	0.91[AMR][1000 genomes]
rs35068861	0.90[AMR][1000 genomes]
rs35123057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35560196	0.91[AMR][1000 genomes]
rs3945	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55836299	0.86[AMR][1000 genomes]
rs56306759	0.84[AMR][1000 genomes]
rs6517519	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs6517523	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs6517526	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs6517533	0.87[AMR][1000 genomes]
rs6517538	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes]
rs68004583	0.87[AMR][1000 genomes]
rs7277978	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7280375	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs7282624	0.89[AMR][1000 genomes]
rs7283420	0.81[AMR][1000 genomes]
rs7283516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7283569	0.87[AMR][1000 genomes]
rs7354783	0.87[AMR][1000 genomes]
rs741795	0.93[YRI][hapmap]
rs8127087	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs8128026	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs8128102	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs8128191	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs8128620	0.89[AMR][1000 genomes]
rs8128827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128894	0.91[AMR][1000 genomes]
rs8129147	0.84[AMR][1000 genomes]
rs8129303	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129416	0.87[AMR][1000 genomes]
rs8130984	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs8131965	0.80[AMR][1000 genomes]
rs8132285	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8132295	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs8132333	0.88[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs8132993	0.93[ASW][hapmap];0.86[YRI][hapmap]
rs8133146	0.87[AMR][1000 genomes]
rs8134733	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs914156	0.82[AFR][1000 genomes]
rs9941894	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv979537	chr21:40714343-40716638	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2776309	PSMG1	cis	Esophagus Mucosa	GTEx
rs2776309	HMGN1	cis	lymphoblastoid	seeQTL
rs2776309	BRWD1	cis	cerebellum	SCAN
rs2776309	CLIC6	cis	parietal	SCAN
rs2776309	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2776309	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2776309	BRWD1	cis	parietal	SCAN
rs2776309	PSMG1	cis	lymphoblastoid	seeQTL
rs2776309	HMGN1	cis	multi-tissue	Pritchard
rs2776309	PSMG1	cis	parietal	SCAN

Chromatin state (count:127 , 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	chr21:40704600-40717200	Weak transcription	Right Ventricle	heart
4	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:40711800-40719600	Weak transcription	Pancreas	Pancrea
6	chr21:40712000-40717200	Strong transcription	Fetal Stomach	stomach
7	chr21:40712200-40716000	Strong transcription	Stomach Smooth Muscle	stomach
8	chr21:40712200-40716200	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr21:40712200-40718800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr21:40712400-40715800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr21:40712600-40716000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr21:40712600-40716400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr21:40712600-40716600	Strong transcription	Fetal Brain Female	brain
14	chr21:40712600-40716800	Strong transcription	Dnd41	blood
15	chr21:40712600-40717000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr21:40712600-40717000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr21:40712600-40717000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr21:40712600-40717000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr21:40712600-40717000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr21:40712600-40717200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr21:40712600-40717400	Strong transcription	Fetal Intestine Large	intestine
22	chr21:40712600-40717400	Strong transcription	Fetal Thymus	thymus
23	chr21:40712600-40717400	Strong transcription	Osteobl	bone
24	chr21:40712600-40717600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr21:40712600-40717600	Strong transcription	Fetal Muscle Leg	muscle
26	chr21:40712600-40717600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr21:40712600-40717600	Strong transcription	Thymus	Thymus
28	chr21:40712600-40718200	Strong transcription	HSMM	muscle
29	chr21:40712800-40715800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr21:40712800-40715800	Strong transcription	Brain Germinal Matrix	brain
31	chr21:40712800-40715800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr21:40712800-40716000	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr21:40712800-40716000	Strong transcription	Colonic Mucosa	Colon
34	chr21:40712800-40716000	Strong transcription	Fetal Lung	lung
35	chr21:40712800-40716200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr21:40712800-40716400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr21:40712800-40716400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr21:40712800-40716400	Strong transcription	Left Ventricle	heart
39	chr21:40712800-40716400	Strong transcription	NH-A	brain
40	chr21:40712800-40716600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr21:40712800-40717000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr21:40712800-40717000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr21:40712800-40717000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr21:40712800-40717000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr21:40712800-40717000	Strong transcription	Fetal Kidney	kidney
46	chr21:40712800-40717000	Strong transcription	HMEC	breast
47	chr21:40712800-40717200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr21:40712800-40717200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr21:40712800-40717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr21:40712800-40717400	Strong transcription	Liver	Liver

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