Variant report

Variant	rs13099995
Chromosome Location	chr3:142764009-142764010
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	chr3:142760427..142762094-chr3:142762981..142765806,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10413	0.89[EUR][1000 genomes]
rs1043898	0.88[EUR][1000 genomes]
rs10451867	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10513184	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1053950	0.89[EUR][1000 genomes]
rs10790	0.84[EUR][1000 genomes]
rs10935475	0.81[EUR][1000 genomes]
rs10935479	0.88[EUR][1000 genomes]
rs11915462	0.83[EUR][1000 genomes]
rs11922201	0.85[EUR][1000 genomes]
rs12490776	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12492904	0.82[EUR][1000 genomes]
rs13075955	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13088422	0.91[EUR][1000 genomes]
rs13094293	0.87[EUR][1000 genomes]
rs1349262	0.89[EUR][1000 genomes]
rs13715	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1375814	0.84[EUR][1000 genomes]
rs1449868	0.85[EUR][1000 genomes]
rs1449869	0.89[EUR][1000 genomes]
rs1530753	0.89[EUR][1000 genomes]
rs1532588	0.84[EUR][1000 genomes]
rs17557029	0.82[EUR][1000 genomes]
rs1814565	0.85[EUR][1000 genomes]
rs1827159	0.89[EUR][1000 genomes]
rs1839406	0.85[EUR][1000 genomes]
rs1868569	0.87[EUR][1000 genomes]
rs1868570	0.87[EUR][1000 genomes]
rs1965343	0.84[EUR][1000 genomes]
rs2045306	0.89[EUR][1000 genomes]
rs2124541	0.84[EUR][1000 genomes]
rs2124542	0.81[EUR][1000 genomes]
rs2124543	0.81[EUR][1000 genomes]
rs2137586	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2175739	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2353408	0.86[EUR][1000 genomes]
rs2353409	0.89[EUR][1000 genomes]
rs2353411	0.89[EUR][1000 genomes]
rs3821645	0.89[EUR][1000 genomes]
rs3856697	0.87[EUR][1000 genomes]
rs3902877	0.82[EUR][1000 genomes]
rs4030582	0.85[EUR][1000 genomes]
rs4683444	0.88[EUR][1000 genomes]
rs4683721	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683722	0.85[EUR][1000 genomes]
rs4683723	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683724	0.86[EUR][1000 genomes]
rs56382522	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6440129	0.85[EUR][1000 genomes]
rs6440131	0.88[EUR][1000 genomes]
rs6440132	0.86[EUR][1000 genomes]
rs6440133	0.80[EUR][1000 genomes]
rs6440134	0.89[EUR][1000 genomes]
rs6770102	0.81[EUR][1000 genomes]
rs6778454	0.81[EUR][1000 genomes]
rs6781080	0.85[EUR][1000 genomes]
rs6781887	0.84[EUR][1000 genomes]
rs6783145	0.86[EUR][1000 genomes]
rs6796771	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6805417	0.88[EUR][1000 genomes]
rs6806551	0.87[EUR][1000 genomes]
rs6808689	0.85[EUR][1000 genomes]
rs7611721	0.85[EUR][1000 genomes]
rs7623532	0.88[EUR][1000 genomes]
rs7644475	0.83[EUR][1000 genomes]
rs7648143	0.87[EUR][1000 genomes]
rs7649225	0.82[EUR][1000 genomes]
rs7652745	0.83[EUR][1000 genomes]
rs766360	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs936194	0.89[EUR][1000 genomes]
rs936196	0.89[EUR][1000 genomes]
rs936197	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937498	0.87[EUR][1000 genomes]
rs9814656	0.88[EUR][1000 genomes]
rs9816317	0.89[EUR][1000 genomes]
rs9835348	0.85[EUR][1000 genomes]
rs9847059	0.87[EUR][1000 genomes]
rs9851353	0.87[EUR][1000 genomes]
rs9862433	0.86[EUR][1000 genomes]
rs9877128	0.88[EUR][1000 genomes]
rs9877135	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13099995	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142727400-142764400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:142728600-142769000	Weak transcription	Pancreas	Pancrea
3	chr3:142729200-142765000	Strong transcription	Dnd41	blood
4	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
5	chr3:142729400-142764800	Strong transcription	K562	blood
6	chr3:142729800-142764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:142729800-142765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:142730200-142765000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:142730200-142765000	Strong transcription	Fetal Thymus	thymus
10	chr3:142732800-142765000	Strong transcription	HSMM	muscle
11	chr3:142733200-142764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
13	chr3:142740000-142769200	Weak transcription	Gastric	stomach
14	chr3:142742400-142764800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:142742600-142764200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:142743600-142764400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:142749000-142784200	Weak transcription	Small Intestine	intestine
18	chr3:142749200-142765000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:142749200-142769000	Weak transcription	Right Ventricle	heart
20	chr3:142749200-142779000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:142754200-142769800	Weak transcription	Colonic Mucosa	Colon
22	chr3:142755200-142764800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:142755400-142764800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:142755800-142765000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr3:142755800-142765000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:142755800-142765000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:142756000-142774400	Weak transcription	Stomach Mucosa	stomach
28	chr3:142756200-142769200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:142759800-142764400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:142759800-142765000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:142760000-142765000	Strong transcription	Hela-S3	cervix
32	chr3:142760600-142764200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:142760600-142764400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:142760600-142764600	Strong transcription	A549	lung
35	chr3:142760600-142764800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:142760600-142764800	Strong transcription	Primary T cells from cord blood	blood
37	chr3:142760600-142764800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:142760600-142764800	Strong transcription	HMEC	breast
39	chr3:142760600-142765000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:142760800-142764800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:142760800-142764800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr3:142760800-142764800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:142760800-142764800	Strong transcription	Adipose Nuclei	Adipose
44	chr3:142760800-142764800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:142760800-142765000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:142760800-142765000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:142760800-142765000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr3:142760800-142765600	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr3:142761000-142764800	Strong transcription	Fetal Intestine Large	intestine
50	chr3:142761000-142765000	Strong transcription	Placenta	Placenta

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