Variant report

Variant	rs10413
Chromosome Location	chr3:142779294-142779295
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	chr3:142771385..142780409-chr3:142780501..142789449,10	K562	blood:
2	chr3:142773649..142775353-chr3:142777692..142779387,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1043898	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10451867	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10513184	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1053950	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10790	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935475	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10935479	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11709036	0.80[EUR][1000 genomes]
rs11915462	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11922201	0.90[EUR][1000 genomes]
rs12485790	0.87[EUR][1000 genomes]
rs12490776	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12492904	0.93[EUR][1000 genomes]
rs12695770	0.87[EUR][1000 genomes]
rs13075955	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13088422	0.88[EUR][1000 genomes]
rs13094293	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13099995	0.89[EUR][1000 genomes]
rs1349262	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13715	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1375814	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1449868	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1449869	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1530753	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1532588	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1545597	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17557029	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1814565	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1827159	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1839406	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1868569	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1868570	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1965343	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2045306	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2124541	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2124542	0.92[EUR][1000 genomes]
rs2124543	0.92[EUR][1000 genomes]
rs2137586	0.92[EUR][1000 genomes]
rs2175739	0.92[EUR][1000 genomes]
rs2290549	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2353408	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2353409	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353411	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821645	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3856697	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3902877	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4030582	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683444	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683721	0.93[EUR][1000 genomes]
rs4683722	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683723	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683724	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56382522	0.91[EUR][1000 genomes]
rs6440129	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440131	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440132	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440133	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440134	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6770102	0.92[EUR][1000 genomes]
rs6778454	0.92[EUR][1000 genomes]
rs6781080	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6781887	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6783145	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784200	0.84[EUR][1000 genomes]
rs6796771	0.88[EUR][1000 genomes]
rs6802376	0.82[EUR][1000 genomes]
rs6805417	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6806551	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6808406	0.83[EUR][1000 genomes]
rs6808689	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611721	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7623532	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7644475	0.87[EUR][1000 genomes]
rs7648143	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649225	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7652745	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766360	0.90[EUR][1000 genomes]
rs936194	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936196	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936197	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs937498	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814656	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9816317	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9820175	0.83[EUR][1000 genomes]
rs9831162	0.84[EUR][1000 genomes]
rs9835348	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9847059	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9851353	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862433	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9875210	0.84[EUR][1000 genomes]
rs9877128	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9877135	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1004467	chr3:142768867-142800605	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1004682	chr3:142768867-142804154	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10413	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
2	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
3	chr3:142749000-142784200	Weak transcription	Small Intestine	intestine
4	chr3:142763400-142787000	Weak transcription	Spleen	Spleen
5	chr3:142764200-142784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:142764800-142779600	Weak transcription	Fetal Brain Male	brain
7	chr3:142765000-142782200	Weak transcription	Fetal Heart	heart
8	chr3:142765400-142791600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:142766800-142780800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:142766800-142780800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:142766800-142781000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:142766800-142781600	Strong transcription	Dnd41	blood
13	chr3:142767400-142781400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:142767400-142786600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:142769200-142782800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:142769600-142789000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:142770400-142787000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:142771200-142781800	Weak transcription	Lung	lung
19	chr3:142771200-142790000	Weak transcription	Pancreas	Pancrea
20	chr3:142771400-142786600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:142771600-142780400	Weak transcription	Right Ventricle	heart
22	chr3:142771600-142786600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:142772200-142784800	Weak transcription	Fetal Stomach	stomach
24	chr3:142773000-142783200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:142773000-142783400	Weak transcription	Colonic Mucosa	Colon
26	chr3:142773000-142783400	Weak transcription	Left Ventricle	heart
27	chr3:142773000-142783400	Weak transcription	Thymus	Thymus
28	chr3:142773000-142790200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:142773400-142785200	Weak transcription	Fetal Kidney	kidney
30	chr3:142773400-142788800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:142774000-142780200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:142774000-142780400	Weak transcription	Brain Germinal Matrix	brain
33	chr3:142774000-142781800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:142774000-142785200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:142774000-142785800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:142774200-142782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:142774200-142784200	Weak transcription	Ovary	ovary
38	chr3:142774200-142789400	Weak transcription	NHLF	lung
39	chr3:142774400-142785200	Weak transcription	Fetal Brain Female	brain
40	chr3:142775000-142786400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:142775200-142781800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:142775200-142789200	Weak transcription	NHDF-Ad	bronchial
43	chr3:142775400-142781800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:142775400-142781800	Weak transcription	Fetal Lung	lung
45	chr3:142775400-142782000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:142775400-142782000	Weak transcription	Brain Anterior Caudate	brain
47	chr3:142775400-142783000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:142775400-142786000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:142775400-142786200	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:142775400-142786600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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