Variant report

Variant	rs4642169
Chromosome Location	chr3:121560223-121560224
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	chr3:121559897..121561834-chr3:121567497..121569683,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs1135750	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11716027	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486499	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12695416	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13074133	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13096164	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1574036	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1881994	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1920293	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1920296	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1920321	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1920323	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2331964	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2331965	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3934935	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4073474	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4257594	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4257595	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4543051	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4582090	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4645167	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4676693	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4676694	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4676743	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676744	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676745	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676746	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676747	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676748	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676749	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4676750	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4676752	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4676753	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4676755	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4676756	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6438652	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6438655	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6438656	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6438662	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438663	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438664	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438665	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438666	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6438669	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438675	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438677	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438678	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438679	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6766280	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6766694	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6771049	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6771158	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6775544	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6780316	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6781175	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6781604	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6782082	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6783659	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6783781	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6789860	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6793073	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6795182	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6797347	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6798415	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6802715	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6802815	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6804757	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6808500	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6809737	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7612211	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7612301	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7619226	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7623662	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7623743	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7624494	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7625529	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7626574	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7628439	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7632786	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7642353	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7649273	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9824133	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9824198	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9834039	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9834471	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9854539	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9877946	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9878426	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9882971	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv933192	chr3:121544496-121575871	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4642169	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs4642169	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs4642169	IQCB1	cis	Whole Blood	GTEx
rs4642169	IQCB1	cis	multi-tissue	Pritchard
rs4642169	IQCB1	cis	Thyroid	GTEx
rs4642169	IQCB1	cis	Esophagus Muscularis	GTEx
rs4642169	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs4642169	IQCB1	cis	Artery Tibial	GTEx
rs4642169	CD86	Cis_1M	lymphoblastoid	RTeQTL
rs4642169	SLC15A2	cis	multi-tissue	Pritchard
rs4642169	IQCB1	cis	lung	GTEx
rs4642169	EAF2	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121554600-121566800	Weak transcription	Spleen	Spleen
2	chr3:121554800-121561800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:121554800-121570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:121554800-121576600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:121554800-121581800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:121554800-121583400	Weak transcription	Psoas Muscle	Psoas
7	chr3:121554800-121604000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:121555000-121571000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:121555000-121585600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:121555000-121592600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:121555000-121593400	Weak transcription	Liver	Liver
12	chr3:121555200-121592000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:121555600-121563600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:121555600-121568200	Weak transcription	Fetal Thymus	thymus
15	chr3:121555600-121569600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:121555600-121582000	Weak transcription	Thymus	Thymus
17	chr3:121555600-121586200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:121555600-121593800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:121555800-121615600	Weak transcription	Primary T cells from cord blood	blood
20	chr3:121556600-121581600	Weak transcription	Fetal Intestine Small	intestine
21	chr3:121556600-121591400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:121557000-121562000	Weak transcription	Fetal Lung	lung
23	chr3:121557200-121561200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:121557200-121563200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr3:121557600-121561000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:121557600-121563800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:121558400-121563600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:121558800-121565400	Weak transcription	Primary B cells from cord blood	blood
29	chr3:121559000-121563200	Weak transcription	GM12878-XiMat	blood
30	chr3:121559200-121563400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:121559200-121613200	Weak transcription	Brain Angular Gyrus	brain
32	chr3:121559400-121562800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:121559600-121563400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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