Variant report

Variant	rs1530753
Chromosome Location	chr3:142758092-142758093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142752534..142757163-chr3:142757790..142760987,5	K562	blood:
2	chr3:142718831..142720349-chr3:142757842..142760220,2	MCF-7	breast:
3	chr3:142758048..142759562-chr3:142771594..142774382,2	K562	blood:
4	chr3:142755305..142760138-chr3:142835756..142840820,6	K562	blood:
5	chr3:142745390..142747249-chr3:142757780..142759686,2	K562	blood:
6	chr3:142755375..142756882-chr3:142757449..142760432,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268129	Chromatin interaction
ENSG00000175040	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10413	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1043898	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10451867	0.95[EUR][1000 genomes]
rs10513184	0.96[CEU][hapmap];0.86[CHB][hapmap];0.96[EUR][1000 genomes]
rs1053950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10790	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935475	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935479	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11709036	0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[EUR][1000 genomes]
rs11915462	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11922201	0.90[EUR][1000 genomes]
rs12485790	0.87[EUR][1000 genomes]
rs12490776	0.95[EUR][1000 genomes]
rs12492904	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12695770	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13075955	0.95[EUR][1000 genomes]
rs13088422	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13094293	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13099995	0.89[EUR][1000 genomes]
rs1349262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13715	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[EUR][1000 genomes]
rs1375814	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1449868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1449869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545597	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17557029	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1814565	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs1827159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1868569	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1868570	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1965343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2045306	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2124541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124542	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2124543	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2137586	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs2175739	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs2290549	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353408	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2353409	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856697	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3902877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4030582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683444	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683721	0.93[EUR][1000 genomes]
rs4683722	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683723	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683724	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56382522	0.91[EUR][1000 genomes]
rs6440129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440131	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440132	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440133	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6770102	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6778454	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6781080	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6781887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783145	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784200	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs6796771	0.88[EUR][1000 genomes]
rs6802376	0.82[EUR][1000 genomes]
rs6805417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6806551	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6808406	0.83[EUR][1000 genomes]
rs6808689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623532	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7644475	0.87[EUR][1000 genomes]
rs7648143	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7649225	0.93[EUR][1000 genomes]
rs7652745	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766360	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes]
rs936194	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936196	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936197	0.95[EUR][1000 genomes]
rs937498	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814656	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9816317	0.86[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	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9847059	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9851353	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862433	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9875210	0.84[EUR][1000 genomes]
rs9877128	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9877135	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1530753	SR140	cis	Lymphoblastoid	GTEx
rs1530753	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	chr3:142721800-142761800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:142727400-142764400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:142728600-142769000	Weak transcription	Pancreas	Pancrea
4	chr3:142729200-142758600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:142729200-142765000	Strong transcription	Dnd41	blood
6	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
7	chr3:142729400-142764800	Strong transcription	K562	blood
8	chr3:142729800-142764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:142729800-142765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:142730200-142765000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:142730200-142765000	Strong transcription	Fetal Thymus	thymus
12	chr3:142730800-142758800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:142732800-142759000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:142732800-142765000	Strong transcription	HSMM	muscle
15	chr3:142733200-142764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:142734000-142758800	Strong transcription	Liver	Liver
17	chr3:142734400-142759000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
19	chr3:142734600-142758800	Strong transcription	GM12878-XiMat	blood
20	chr3:142735000-142758800	Strong transcription	Placenta	Placenta
21	chr3:142735600-142759400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr3:142735600-142759400	Strong transcription	NHDF-Ad	bronchial
23	chr3:142735800-142758600	Strong transcription	Primary hematopoietic stem cells	blood
24	chr3:142740000-142769200	Weak transcription	Gastric	stomach
25	chr3:142740200-142763200	Weak transcription	Lung	lung
26	chr3:142742400-142764800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:142742600-142764200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:142743600-142763200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:142743600-142764400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:142744600-142759400	Strong transcription	Primary T cells from cord blood	blood
31	chr3:142745800-142758800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr3:142746000-142758400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr3:142746000-142759400	Strong transcription	Primary B cells from cord blood	blood
34	chr3:142747000-142761800	Weak transcription	Fetal Brain Male	brain
35	chr3:142748800-142762000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:142749000-142761800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:142749000-142762000	Weak transcription	Spleen	Spleen
38	chr3:142749000-142763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:142749000-142784200	Weak transcription	Small Intestine	intestine
40	chr3:142749200-142758800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:142749200-142759000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:142749200-142762000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:142749200-142763000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:142749200-142763600	Weak transcription	Psoas Muscle	Psoas
45	chr3:142749200-142765000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:142749200-142769000	Weak transcription	Right Ventricle	heart
47	chr3:142749200-142779000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:142749600-142761600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:142750400-142762000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:142751200-142762600	Weak transcription	Fetal Intestine Small	intestine

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