Variant report

Variant	rs2078203
Chromosome Location	chr21:47881309-47881310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47879910..47881724-chr21:47920617..47924797,3	K562	blood:
2	chr21:47639323..47641508-chr21:47879024..47881708,2	MCF-7	breast:
3	chr21:47706221..47707965-chr21:47878068..47881386,3	K562	blood:
4	chr21:47647621..47651234-chr21:47875652..47881416,7	K562	blood:
5	chr21:47879656..47881987-chr21:47889177..47890960,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160305	Chromatin interaction
ENSG00000160285	Chromatin interaction
ENSG00000215424	Chromatin interaction
ENSG00000182362	Chromatin interaction
ENSG00000223901	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1010111	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10854482	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11089076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11701286	0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11701512	0.85[ASN][1000 genomes]
rs12627695	1.00[JPT][hapmap]
rs13047696	0.81[JPT][hapmap]
rs13047818	0.89[ASN][1000 genomes]
rs13053115	0.91[ASN][1000 genomes]
rs17371795	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1981330	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016807	0.86[ASN][1000 genomes]
rs2032110	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2070429	0.81[JPT][hapmap]
rs2070431	0.81[JPT][hapmap]
rs2073378	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs2239574	0.81[JPT][hapmap]
rs2249060	0.86[CHB][hapmap]
rs2330591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2330592	0.84[ASN][1000 genomes]
rs2839222	0.86[CHB][hapmap]
rs2839224	0.86[CHB][hapmap]
rs2839232	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap]
rs2839235	0.93[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap]
rs2839251	0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2839262	0.93[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2839267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2839273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2839274	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839283	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2839289	0.92[ASN][1000 genomes]
rs2839292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2839298	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs2839305	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs2839321	0.87[JPT][hapmap]
rs34722617	0.81[JPT][hapmap]
rs35418111	0.81[ASN][1000 genomes]
rs4143362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4818837	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4818846	0.81[JPT][hapmap]
rs57385578	0.83[ASN][1000 genomes]
rs62224255	0.96[ASN][1000 genomes]
rs71326328	0.94[ASN][1000 genomes]
rs7275926	0.91[ASN][1000 genomes]
rs7276409	0.97[ASN][1000 genomes]
rs7277463	0.87[ASN][1000 genomes]
rs7279052	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7279193	0.86[CHB][hapmap]
rs7280077	0.99[ASN][1000 genomes]
rs7282126	0.81[JPT][hapmap]
rs7282296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs762251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8126917	0.93[ASN][1000 genomes]
rs8127280	0.81[JPT][hapmap]
rs8129188	0.84[ASN][1000 genomes]
rs8130538	0.99[ASN][1000 genomes]
rs8132320	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8134014	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8134832	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9306152	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs9637222	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9637223	0.86[ASN][1000 genomes]
rs9712582	0.95[ASN][1000 genomes]
rs9979185	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9979962	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9981192	0.96[ASN][1000 genomes]
rs9983522	0.95[ASN][1000 genomes]
rs9983528	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
2	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
3	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
4	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
5	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
6	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
7	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
9	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
10	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
11	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
12	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
13	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
14	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
15	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
16	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
17	nsv914136	chr21:47681041-47900994	Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	n/a
18	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
19	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
20	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
21	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
22	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
23	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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	30 gene(s)	inside rSNPs	n/a
24	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
25	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
26	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
27	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2078203	C21orf57	cis	multi-tissue	Pritchard
rs2078203	S100B	cis	cerebellum	SCAN
rs2078203	S100B	cis	parietal	SCAN
rs2078203	PCNT	cis	lymphoblastoid	seeQTL
rs2078203	YBEY	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47879800-47892000	Weak transcription	Lung	lung
2	chr21:47880000-47881600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr21:47880000-47882600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr21:47880000-47882600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr21:47880000-47887600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr21:47880000-47889400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:47880000-47892000	Weak transcription	Liver	Liver
8	chr21:47880000-47892000	Weak transcription	Small Intestine	intestine
9	chr21:47880000-47892200	Weak transcription	Pancreas	Pancrea
10	chr21:47880000-47892200	Weak transcription	Spleen	Spleen
11	chr21:47880000-47892400	Weak transcription	Gastric	stomach
12	chr21:47880000-47900200	Weak transcription	Esophagus	oesophagus
13	chr21:47880000-47900400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr21:47880000-47905800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr21:47880000-47916800	Weak transcription	Aorta	Aorta
16	chr21:47880200-47881800	Weak transcription	Ovary	ovary
17	chr21:47880200-47881800	Weak transcription	Psoas Muscle	Psoas
18	chr21:47880200-47882000	Weak transcription	Right Atrium	heart
19	chr21:47880200-47882400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr21:47880200-47882400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr21:47880200-47882600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr21:47880200-47882600	Weak transcription	Placenta	Placenta
23	chr21:47880200-47882600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr21:47880200-47882800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr21:47880200-47882800	Weak transcription	Fetal Thymus	thymus
26	chr21:47880200-47883200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr21:47880200-47883400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr21:47880200-47886000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr21:47880200-47889000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr21:47880200-47889400	Weak transcription	Fetal Intestine Small	intestine
31	chr21:47880200-47892400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr21:47880200-47900000	Weak transcription	Colonic Mucosa	Colon
33	chr21:47880200-47902800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr21:47880200-47903200	Weak transcription	Stomach Mucosa	stomach
35	chr21:47880200-47909400	Weak transcription	A549	lung
36	chr21:47880200-47911600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr21:47880200-47916600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr21:47880400-47881400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr21:47880400-47881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr21:47880400-47881400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr21:47880400-47881600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr21:47880400-47881600	Weak transcription	Colon Smooth Muscle	Colon
43	chr21:47880400-47881600	Weak transcription	Fetal Muscle Leg	muscle
44	chr21:47880400-47881800	Weak transcription	Adipose Nuclei	Adipose
45	chr21:47880400-47881800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr21:47880400-47882000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr21:47880400-47882000	Weak transcription	Brain Germinal Matrix	brain
48	chr21:47880400-47882200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr21:47880400-47882200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr21:47880400-47882200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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