Variant report

Variant	rs7248577
Chromosome Location	chr19:39208795-39208796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39197861..39200154-chr19:39208243..39210310,2	MCF-7	breast:
2	chr19:39207119..39209379-chr19:39340963..39342887,2	K562	blood:
3	chr19:39141347..39144030-chr19:39208371..39211834,3	MCF-7	breast:
4	chr19:39207779..39209795-chr19:39227154..39229627,2	MCF-7	breast:
5	chr19:39202818..39205555-chr19:39206868..39209450,2	K562	blood:
6	chr19:39207862..39211804-chr19:39330654..39334530,3	MCF-7	breast:
7	chr19:39196541..39198571-chr19:39208360..39211296,2	K562	blood:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000267892	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1105759	0.89[ASN][1000 genomes]
rs1106372	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1136956	0.97[ASN][1000 genomes]
rs12971309	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12972987	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12972997	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12974733	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975079	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12975953	0.96[AMR][1000 genomes]
rs12976598	1.00[AMR][1000 genomes]
rs12977238	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12978273	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12978715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12978914	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12979947	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980399	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12981131	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12983010	0.87[EUR][1000 genomes]
rs12983550	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12984794	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12985030	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12985558	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12985871	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12986032	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12986121	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12986337	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2001856	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2086148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126970	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279146	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34026184	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054765	1.00[AMR][1000 genomes]
rs34082501	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34083318	0.82[ASN][1000 genomes]
rs34105297	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34126343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34134906	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34305426	1.00[AMR][1000 genomes]
rs34332511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34368672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34525537	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34558140	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34563817	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34592527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34695688	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34703567	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34717167	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34843929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34862518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34899634	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34911882	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35007285	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35074956	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35096737	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35134120	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35193699	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35281901	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35403788	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35436155	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35576862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35640008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35666464	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35685980	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35691365	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35716073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35729716	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35807146	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35855940	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35856174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35941349	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3786840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45599933	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56817884	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56946356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57230275	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60454376	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61121905	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62119101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119105	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62119109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62119115	0.97[ASN][1000 genomes]
rs62119116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120068	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120072	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62120074	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62121811	0.82[ASN][1000 genomes]
rs62121819	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62121821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62121823	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62121827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62121829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71356822	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246368	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7260070	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103530	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8104815	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105080	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8105216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105550	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs899199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs899200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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	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
2	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
3	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
4	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
5	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
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv911669	chr19:39196745-39231548	Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7248577	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39186400-39213400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:39189400-39223400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:39189800-39222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:39190000-39208800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:39190000-39218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:39190200-39222600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:39190200-39222800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:39190400-39209200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr19:39190400-39212000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:39190400-39212200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:39190400-39217000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr19:39190400-39218000	Strong transcription	Primary T cells from cord blood	blood
15	chr19:39190400-39222400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:39190400-39222600	Strong transcription	Dnd41	blood
17	chr19:39190600-39209000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr19:39190600-39209200	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr19:39190600-39216400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr19:39190600-39217000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:39190600-39219600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr19:39190600-39222800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:39190800-39220400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:39190800-39222600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr19:39190800-39222600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:39190800-39222800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr19:39190800-39223000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:39190800-39223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:39191000-39222400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr19:39191000-39222600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr19:39191400-39209400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:39191400-39218800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:39192400-39221200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:39192800-39209600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:39193400-39210200	Strong transcription	Brain Germinal Matrix	brain
36	chr19:39199000-39215600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:39199000-39220400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr19:39199400-39215400	Weak transcription	Fetal Kidney	kidney
39	chr19:39199800-39214600	Strong transcription	HUVEC	blood vessel
40	chr19:39200200-39209400	Strong transcription	Fetal Intestine Large	intestine
41	chr19:39200400-39217200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:39202400-39209400	Strong transcription	Colonic Mucosa	Colon
43	chr19:39202800-39221400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr19:39203000-39209200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:39203000-39209200	Strong transcription	NHEK	skin
46	chr19:39203200-39209200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:39203200-39209400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:39203400-39209200	Strong transcription	NH-A	brain
49	chr19:39203400-39218600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:39204000-39209600	Strong transcription	Osteobl	bone

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