Variant report

Variant	rs1980689
Chromosome Location	chr10:112577242-112577243
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:112575848..112579708-chr10:112630463..112632993,4	MCF-7	breast:
2	chr10:112566469..112571087-chr10:112574225..112578785,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203497	Chromatin interaction
ENSG00000150593	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10736209	0.84[AMR][1000 genomes]
rs10787283	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10885052	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10885053	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10885054	0.83[CEU][hapmap]
rs10885055	0.92[CEU][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes]
rs11195340	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1832745	0.82[EUR][1000 genomes]
rs1923807	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4918595	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4918598	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4918599	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4918600	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4918601	0.87[CEU][hapmap];0.86[YRI][hapmap]
rs7072681	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs726803	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs726804	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7922732	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1980689	PDCD4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112558000-112578400	Weak transcription	Aorta	Aorta
2	chr10:112564000-112581600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:112564200-112579200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:112568600-112577400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:112569000-112578000	Weak transcription	Colonic Mucosa	Colon
6	chr10:112572200-112577600	Weak transcription	Adipose Nuclei	Adipose
7	chr10:112572600-112593800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:112572800-112577800	Genic enhancers	Fetal Heart	heart
9	chr10:112572800-112581400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:112572800-112582200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr10:112573000-112578800	Enhancers	Primary T cells from cord blood	blood
12	chr10:112573200-112577400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr10:112573200-112578200	Weak transcription	Placenta	Placenta
14	chr10:112573400-112580800	Weak transcription	K562	blood
15	chr10:112574000-112578000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr10:112574400-112578400	Weak transcription	Small Intestine	intestine
17	chr10:112574600-112578200	Weak transcription	Liver	Liver
18	chr10:112574600-112579000	Enhancers	GM12878-XiMat	blood
19	chr10:112574800-112579200	Enhancers	Fetal Thymus	thymus
20	chr10:112575000-112577400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr10:112575000-112579800	Enhancers	Stomach Smooth Muscle	stomach
22	chr10:112575200-112577800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr10:112575200-112577800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr10:112575200-112577800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr10:112575200-112577800	Enhancers	Thymus	Thymus
26	chr10:112575200-112582400	Enhancers	Esophagus	oesophagus
27	chr10:112575400-112579400	Genic enhancers	Left Ventricle	heart
28	chr10:112575400-112581400	Enhancers	Fetal Muscle Leg	muscle
29	chr10:112575600-112577600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:112575600-112577800	Genic enhancers	Right Ventricle	heart
31	chr10:112575600-112578200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr10:112575800-112578200	Weak transcription	Fetal Intestine Small	intestine
33	chr10:112575800-112578200	Enhancers	Fetal Muscle Trunk	muscle
34	chr10:112575800-112578400	Weak transcription	Fetal Intestine Large	intestine
35	chr10:112575800-112583600	Enhancers	Right Atrium	heart
36	chr10:112576000-112577800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr10:112576000-112579800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr10:112576000-112580000	Weak transcription	Lung	lung
39	chr10:112576200-112577400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr10:112576200-112577600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr10:112576200-112577600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr10:112576200-112583200	Enhancers	Pancreas	Pancrea
43	chr10:112576400-112577600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr10:112576600-112577800	Enhancers	Primary B cells from peripheral blood	blood
45	chr10:112576600-112580600	Enhancers	Stomach Mucosa	stomach
46	chr10:112576800-112577600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:112576800-112578200	Enhancers	Primary B cells from cord blood	blood
48	chr10:112576800-112578200	Weak transcription	HSMMtube	muscle
49	chr10:112576800-112580600	Enhancers	Rectal Smooth Muscle	rectum
50	chr10:112576800-112584800	Enhancers	Psoas Muscle	Psoas

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