Variant report

Variant	rs6440129
Chromosome Location	chr3:142745293-142745294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:142744068-142747193	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142719836..142721441-chr3:142742742..142745727,2	K562	blood:

Variant related genes	Relation type
U2SURP	TF binding region
ENSG00000163714	Chromatin interaction
ENSG00000268129	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10413	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1043898	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10451867	0.91[EUR][1000 genomes]
rs10513184	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs1053950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10790	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935475	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10935479	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11709036	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs11915462	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11922201	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12485790	0.89[EUR][1000 genomes]
rs12490776	0.91[EUR][1000 genomes]
rs12492904	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12695770	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13075955	0.91[EUR][1000 genomes]
rs13088422	0.84[EUR][1000 genomes]
rs13094293	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13099995	0.85[EUR][1000 genomes]
rs1349262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13715	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs1375814	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1449868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1530753	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]
rs1532588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545597	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17557029	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1814565	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs1827159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1839406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868569	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1868570	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045306	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124542	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2124543	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2137586	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2175739	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2290549	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353408	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2353409	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821645	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]
rs3856697	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3902877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4030582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683444	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683721	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683722	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683723	0.90[EUR][1000 genomes]
rs4683724	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56382522	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6440131	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440132	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440133	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770102	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6778454	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6781080	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783145	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784200	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs6796771	0.84[EUR][1000 genomes]
rs6802376	0.84[EUR][1000 genomes]
rs6805417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806551	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6808689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623532	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644475	0.89[EUR][1000 genomes]
rs7648143	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7649225	0.89[EUR][1000 genomes]
rs7652745	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs766360	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[EUR][1000 genomes]
rs936194	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936196	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936197	0.91[EUR][1000 genomes]
rs937498	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9814656	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9816317	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9835348	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847059	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9851353	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9862433	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9875210	0.80[EUR][1000 genomes]
rs9877128	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877135	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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
rs6440129	SR140	cis	multi-tissue	Pritchard
rs6440129	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	chr3:142728400-142748400	Weak transcription	Spleen	Spleen
4	chr3:142728600-142769000	Weak transcription	Pancreas	Pancrea
5	chr3:142729200-142758600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:142729200-142765000	Strong transcription	Dnd41	blood
7	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
8	chr3:142729400-142764800	Strong transcription	K562	blood
9	chr3:142729800-142764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:142729800-142765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:142730200-142753400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:142730200-142765000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:142730200-142765000	Strong transcription	Fetal Thymus	thymus
14	chr3:142730400-142754200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr3:142730600-142753800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:142730800-142758800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:142731000-142749400	Strong transcription	Adipose Nuclei	Adipose
18	chr3:142731000-142754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:142731200-142753800	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:142732600-142754200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:142732800-142759000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:142732800-142765000	Strong transcription	HSMM	muscle
23	chr3:142733000-142755000	Weak transcription	Stomach Mucosa	stomach
24	chr3:142733200-142754200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:142733200-142764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:142733400-142750400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:142734000-142758800	Strong transcription	Liver	Liver
28	chr3:142734400-142747800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:142734400-142759000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
31	chr3:142734600-142748400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:142734600-142758800	Strong transcription	GM12878-XiMat	blood
33	chr3:142734800-142756400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:142735000-142749000	Strong transcription	HMEC	breast
35	chr3:142735000-142750800	Strong transcription	A549	lung
36	chr3:142735000-142758800	Strong transcription	Placenta	Placenta
37	chr3:142735200-142750600	Strong transcription	Fetal Lung	lung
38	chr3:142735200-142753400	Strong transcription	NH-A	brain
39	chr3:142735200-142753600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr3:142735200-142754000	Strong transcription	Osteobl	bone
41	chr3:142735600-142753400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:142735600-142759400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:142735600-142759400	Strong transcription	NHDF-Ad	bronchial
44	chr3:142735800-142749000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr3:142735800-142758600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr3:142736800-142745800	Weak transcription	Psoas Muscle	Psoas
47	chr3:142737000-142747800	Weak transcription	Fetal Stomach	stomach
48	chr3:142737200-142747600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:142737200-142748600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:142737200-142748600	Weak transcription	Fetal Intestine Small	intestine

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