Variant report

Variant	rs2298560
Chromosome Location	chr21:40185975-40185976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40184185..40186181-chr21:40274030..40276834,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11701301	0.92[ASN][1000 genomes]
rs11911369	0.89[ASN][1000 genomes]
rs17230954	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17230961	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2410062	1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2836715	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2836717	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2836720	0.92[ASN][1000 genomes]
rs2836724	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs28420538	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs28508188	0.92[ASN][1000 genomes]
rs28817686	0.92[ASN][1000 genomes]
rs28836833	0.92[ASN][1000 genomes]
rs414845	0.82[JPT][hapmap]
rs467698	0.92[ASN][1000 genomes]
rs467806	0.92[ASN][1000 genomes]
rs57740627	0.89[ASN][1000 genomes]
rs59086904	0.92[ASN][1000 genomes]
rs60328145	0.86[ASN][1000 genomes]
rs714780	0.89[ASN][1000 genomes]
rs7278693	0.96[ASN][1000 genomes]
rs7279299	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7283433	0.96[ASN][1000 genomes]
rs73450548	0.89[ASN][1000 genomes]
rs73450552	0.89[ASN][1000 genomes]
rs8128181	0.86[ASN][1000 genomes]
rs8133056	0.86[ASN][1000 genomes]
rs8133164	0.86[ASN][1000 genomes]
rs8134019	0.86[ASN][1000 genomes]
rs8134441	0.86[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	nsv1058591	chr21:40114130-40190594	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2298560	NCRNA00257	cis	parietal	SCAN
rs2298560	MX1	cis	cerebellum	SCAN
rs2298560	ETS2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40180000-40186200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr21:40180200-40186200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr21:40180200-40198400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr21:40180400-40186400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:40180400-40186400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr21:40180400-40186600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr21:40180600-40186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr21:40180600-40188400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr21:40181000-40186200	Weak transcription	Brain Angular Gyrus	brain
10	chr21:40181000-40186400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr21:40181200-40187400	Strong transcription	Primary T cells from cord blood	blood
12	chr21:40181600-40189000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr21:40181600-40192600	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr21:40181600-40193600	Strong transcription	Fetal Muscle Leg	muscle
15	chr21:40181800-40186200	Weak transcription	Esophagus	oesophagus
16	chr21:40181800-40186400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:40181800-40187400	Genic enhancers	HepG2	liver
18	chr21:40181800-40188400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr21:40181800-40189400	Strong transcription	Placenta	Placenta
20	chr21:40181800-40193800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr21:40181800-40197000	Strong transcription	Fetal Thymus	thymus
22	chr21:40182000-40196600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr21:40182200-40187200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
24	chr21:40182400-40186400	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr21:40182600-40186800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr21:40182600-40189400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr21:40182800-40186200	Weak transcription	Primary B cells from cord blood	blood
28	chr21:40183000-40186200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr21:40183000-40186400	Strong transcription	NHLF	lung
30	chr21:40183000-40186600	Genic enhancers	Rectal Mucosa Donor 31	rectum
31	chr21:40183000-40187200	Genic enhancers	Fetal Intestine Small	intestine
32	chr21:40183000-40196600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr21:40183200-40189600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr21:40183400-40186200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr21:40183400-40186600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
36	chr21:40183600-40186000	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr21:40183600-40186800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
38	chr21:40183600-40196800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr21:40183800-40186000	Strong transcription	Lung	lung
40	chr21:40183800-40186800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr21:40183800-40186800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr21:40183800-40189400	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr21:40183800-40196800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr21:40184000-40186200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr21:40184000-40186400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr21:40184000-40186400	Weak transcription	HSMM	muscle
47	chr21:40184000-40186600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr21:40184000-40187000	Genic enhancers	Dnd41	blood
49	chr21:40184000-40189400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr21:40184000-40192400	Strong transcription	Primary monocytes fromperipheralblood	blood

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