Variant report

Variant	rs7644475
Chromosome Location	chr3:142726135-142726136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142585981..142587495-chr3:142725915..142728856,2	MCF-7	breast:
2	chr3:142725156..142728605-chr3:142735600..142739451,5	MCF-7	breast:
3	chr3:142718194..142723452-chr3:142723791..142728813,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268129	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10413	0.87[EUR][1000 genomes]
rs1043898	0.86[EUR][1000 genomes]
rs10451867	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10513184	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1053950	0.87[EUR][1000 genomes]
rs10790	0.81[EUR][1000 genomes]
rs10935475	0.88[EUR][1000 genomes]
rs10935479	0.86[EUR][1000 genomes]
rs11915462	0.90[EUR][1000 genomes]
rs11922201	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12485790	0.82[EUR][1000 genomes]
rs12490776	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12492904	0.88[EUR][1000 genomes]
rs12695770	0.83[EUR][1000 genomes]
rs13075955	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13094293	0.85[EUR][1000 genomes]
rs13099995	0.83[EUR][1000 genomes]
rs1349262	0.87[EUR][1000 genomes]
rs13715	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1375814	0.91[EUR][1000 genomes]
rs1449868	0.90[EUR][1000 genomes]
rs1449869	0.87[EUR][1000 genomes]
rs1530753	0.87[EUR][1000 genomes]
rs1532588	0.89[EUR][1000 genomes]
rs1545597	0.84[EUR][1000 genomes]
rs17557029	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1814565	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1827159	0.87[EUR][1000 genomes]
rs1839406	0.90[EUR][1000 genomes]
rs1868569	0.85[EUR][1000 genomes]
rs1868570	0.85[EUR][1000 genomes]
rs1965343	0.91[EUR][1000 genomes]
rs2045306	0.87[EUR][1000 genomes]
rs2124541	0.91[EUR][1000 genomes]
rs2124542	0.88[EUR][1000 genomes]
rs2124543	0.88[EUR][1000 genomes]
rs2137586	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2175739	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290549	0.86[EUR][1000 genomes]
rs2353408	0.84[EUR][1000 genomes]
rs2353409	0.87[EUR][1000 genomes]
rs2353411	0.87[EUR][1000 genomes]
rs3821645	0.87[EUR][1000 genomes]
rs3856697	0.85[EUR][1000 genomes]
rs3902877	0.89[EUR][1000 genomes]
rs4030582	0.89[EUR][1000 genomes]
rs4683444	0.86[EUR][1000 genomes]
rs4683721	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683722	0.90[EUR][1000 genomes]
rs4683723	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683724	0.84[EUR][1000 genomes]
rs56382522	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440129	0.89[EUR][1000 genomes]
rs6440131	0.86[EUR][1000 genomes]
rs6440132	0.84[EUR][1000 genomes]
rs6440134	0.87[EUR][1000 genomes]
rs6770102	0.88[EUR][1000 genomes]
rs6778454	0.88[EUR][1000 genomes]
rs6781080	0.90[EUR][1000 genomes]
rs6781887	0.89[EUR][1000 genomes]
rs6783145	0.84[EUR][1000 genomes]
rs6796771	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6805417	0.86[EUR][1000 genomes]
rs6806551	0.85[EUR][1000 genomes]
rs6808689	0.90[EUR][1000 genomes]
rs7611721	0.90[EUR][1000 genomes]
rs7623532	0.86[EUR][1000 genomes]
rs7648143	0.85[EUR][1000 genomes]
rs7649225	0.81[EUR][1000 genomes]
rs7652745	0.81[EUR][1000 genomes]
rs766360	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs936194	0.87[EUR][1000 genomes]
rs936196	0.86[EUR][1000 genomes]
rs936197	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs937498	0.85[EUR][1000 genomes]
rs9814656	0.86[EUR][1000 genomes]
rs9816317	0.87[EUR][1000 genomes]
rs9835348	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9847059	0.85[EUR][1000 genomes]
rs9851353	0.85[EUR][1000 genomes]
rs9862433	0.85[EUR][1000 genomes]
rs9877128	0.86[EUR][1000 genomes]
rs9877135	0.86[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	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	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
4	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7644475	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	chr3:142721200-142727800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:142721400-142735800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:142721600-142727400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:142721600-142728200	Weak transcription	Pancreas	Pancrea
5	chr3:142721600-142739400	Weak transcription	Lung	lung
6	chr3:142721800-142727600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:142721800-142727600	Weak transcription	Left Ventricle	heart
8	chr3:142721800-142728200	Weak transcription	Gastric	stomach
9	chr3:142721800-142730800	Weak transcription	Placenta	Placenta
10	chr3:142721800-142734800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:142721800-142736400	Weak transcription	Ovary	ovary
12	chr3:142721800-142739200	Weak transcription	Colonic Mucosa	Colon
13	chr3:142721800-142761800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:142722000-142726200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:142722000-142726400	Weak transcription	Thymus	Thymus
16	chr3:142722000-142727400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr3:142722000-142727400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:142722000-142729600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr3:142722000-142733000	Weak transcription	Brain Anterior Caudate	brain
20	chr3:142722000-142735800	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:142722000-142735800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:142722000-142737000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:142722000-142739000	Weak transcription	Right Ventricle	heart
24	chr3:142722000-142742400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:142722200-142726800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:142722200-142728200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:142722200-142729000	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:142722200-142729200	Weak transcription	NH-A	brain
29	chr3:142722200-142729400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr3:142722200-142730200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:142722200-142730600	Weak transcription	Fetal Intestine Large	intestine
32	chr3:142722200-142730800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:142722200-142735800	Weak transcription	Brain Germinal Matrix	brain
34	chr3:142722200-142735800	Weak transcription	Fetal Brain Female	brain
35	chr3:142722200-142736400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:142722200-142737000	Weak transcription	Fetal Heart	heart
37	chr3:142722200-142739000	Weak transcription	Brain Angular Gyrus	brain
38	chr3:142722200-142743000	Weak transcription	Brain Substantia Nigra	brain
39	chr3:142722400-142728400	Weak transcription	NHDF-Ad	bronchial
40	chr3:142722400-142728600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:142722400-142729600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr3:142722400-142730400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:142722400-142730400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:142722400-142730400	Weak transcription	HUVEC	blood vessel
45	chr3:142722400-142730600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:142722400-142731000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:142722400-142731000	Weak transcription	Adipose Nuclei	Adipose
48	chr3:142722400-142732800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:142722400-142733200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:142722400-142734600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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