Variant report

Variant	rs60454376
Chromosome Location	chr19:39182899-39182900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39181974..39184740-chr19:39331353..39332941,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1106372	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12971309	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972987	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12972997	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12974733	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12975079	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12975256	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12975953	0.91[AMR][1000 genomes]
rs12976598	0.96[AMR][1000 genomes]
rs12977238	0.83[EUR][1000 genomes]
rs12978273	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12978715	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12978914	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12979947	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12980399	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12981131	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12981984	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12983010	0.87[EUR][1000 genomes]
rs12983550	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12984794	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12985030	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12985558	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12985871	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12986032	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12986121	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12986337	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17589359	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2001856	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2086148	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2126970	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2279145	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279146	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2287728	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34026184	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34054765	0.96[AMR][1000 genomes]
rs34082501	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34105297	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34126343	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34134906	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34305426	0.96[AMR][1000 genomes]
rs34332511	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34368672	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34525537	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34558140	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34563817	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34592527	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34695688	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34703567	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34717167	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34843929	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34862518	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34899634	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911882	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35007285	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35074956	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35096737	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35134120	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35193699	0.83[EUR][1000 genomes]
rs35281901	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35403788	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35436155	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35576862	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35640008	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35666464	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35685980	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35691365	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35716073	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35729716	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35807146	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35855940	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35856174	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35941349	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786840	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45599933	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56817884	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56946356	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57230275	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61121905	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62119101	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119102	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119103	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119105	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62119109	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62119116	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62120068	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62120072	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62120074	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62121819	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62121821	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62121823	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62121827	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121828	0.88[ASN][1000 genomes]
rs62121829	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71356822	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7246368	0.83[EUR][1000 genomes]
rs7248577	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7260070	0.83[EUR][1000 genomes]
rs8103530	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8104815	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8105055	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8105069	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8105080	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105216	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8105550	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899199	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899200	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs973009	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60454376	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
2	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39170000-39183400	Enhancers	Placenta	Placenta
4	chr19:39177000-39183000	Weak transcription	Fetal Brain Female	brain
5	chr19:39177200-39195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:39177400-39183400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:39178000-39183600	Genic enhancers	Muscle Satellite Cultured Cells	--
8	chr19:39178600-39183200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:39178600-39187800	Enhancers	Left Ventricle	heart
10	chr19:39178600-39190600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr19:39178600-39198200	Genic enhancers	Fetal Intestine Large	intestine
12	chr19:39179000-39189400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:39179400-39184400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr19:39179600-39183400	Weak transcription	Primary B cells from cord blood	blood
15	chr19:39179600-39183600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr19:39179800-39183800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:39180000-39183200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr19:39180000-39183800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:39180000-39184800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:39180000-39186000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:39180000-39191600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:39180000-39192400	Genic enhancers	Lung	lung
24	chr19:39180200-39183000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:39180200-39183800	Weak transcription	Hela-S3	cervix
26	chr19:39180400-39183200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:39180600-39183800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:39180600-39185000	Enhancers	NHDF-Ad	bronchial
29	chr19:39180800-39183600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr19:39180800-39183800	Enhancers	HUVEC	blood vessel
31	chr19:39180800-39184800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
32	chr19:39180800-39185000	Enhancers	Pancreas	Pancrea
33	chr19:39180800-39187000	Enhancers	Primary T cells fromperipheralblood	blood
34	chr19:39181000-39183000	Enhancers	Brain Hippocampus Middle	brain
35	chr19:39181000-39183400	Enhancers	Rectal Smooth Muscle	rectum
36	chr19:39181000-39183800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr19:39181000-39183800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:39181000-39184200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr19:39181000-39186600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr19:39181200-39183000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:39181200-39183000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:39181400-39183400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:39181400-39186800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr19:39181600-39183600	Genic enhancers	Duodenum Mucosa	Duodenum
45	chr19:39181600-39183800	Enhancers	Brain Anterior Caudate	brain
46	chr19:39181600-39184800	Enhancers	Brain Substantia Nigra	brain
47	chr19:39181800-39183000	Weak transcription	Aorta	Aorta
48	chr19:39181800-39186400	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr19:39182000-39183400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:39182000-39183600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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