Variant report

Variant	rs12977238
Chromosome Location	chr19:39152530-39152531
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39150052..39153067-chr19:39197622..39201361,3	MCF-7	breast:
2	chr19:39151862..39154243-chr19:39220891..39223454,2	MCF-7	breast:
3	chr19:39150956..39153225-chr19:39190082..39192763,2	MCF-7	breast:
4	chr19:39151900..39153408-chr19:39203433..39205156,2	MCF-7	breast:
5	chr19:39145586..39147740-chr19:39150423..39154465,3	K562	blood:
6	chr19:39150082..39153309-chr19:39178166..39180062,3	MCF-7	breast:
7	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
8	chr19:39151502..39153525-chr19:39175124..39177403,2	MCF-7	breast:
9	chr19:39151359..39154098-chr19:39320807..39323487,3	MCF-7	breast:
10	chr19:39152027..39154763-chr19:39201126..39202967,2	MCF-7	breast:
11	chr19:39151274..39153019-chr19:39209216..39212183,2	MCF-7	breast:
12	chr19:39150654..39152913-chr19:39172186..39173857,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000104823	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs12971309	0.83[EUR][1000 genomes]
rs12974733	0.82[ASN][1000 genomes]
rs12975079	0.82[ASN][1000 genomes]
rs12975256	0.83[EUR][1000 genomes]
rs12977599	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12978715	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12979947	0.82[ASN][1000 genomes]
rs12981131	0.82[ASN][1000 genomes]
rs12981984	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12984794	0.83[EUR][1000 genomes]
rs12985558	0.82[ASN][1000 genomes]
rs12986337	0.82[ASN][1000 genomes]
rs17589359	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2086148	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2126970	0.82[ASN][1000 genomes]
rs2279145	0.83[EUR][1000 genomes]
rs2279146	0.83[EUR][1000 genomes]
rs2287728	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34026184	0.82[ASN][1000 genomes]
rs34082501	0.83[EUR][1000 genomes]
rs34083318	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34105297	0.81[EUR][1000 genomes]
rs34126343	0.83[EUR][1000 genomes]
rs34134906	0.82[ASN][1000 genomes]
rs34332511	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34368672	0.83[EUR][1000 genomes]
rs34525537	0.93[ASN][1000 genomes]
rs34558140	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34563817	0.82[ASN][1000 genomes]
rs34592527	0.83[EUR][1000 genomes]
rs34695688	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34703567	0.82[ASN][1000 genomes]
rs34717167	0.82[ASN][1000 genomes]
rs34843929	0.83[EUR][1000 genomes]
rs34862518	0.83[EUR][1000 genomes]
rs34899634	0.83[EUR][1000 genomes]
rs35074956	0.83[EUR][1000 genomes]
rs35193699	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35281901	0.82[ASN][1000 genomes]
rs35436155	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35488280	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35576862	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35640008	0.83[EUR][1000 genomes]
rs35666464	0.83[EUR][1000 genomes]
rs35685980	0.83[EUR][1000 genomes]
rs35691365	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35716073	0.83[EUR][1000 genomes]
rs35729716	0.83[EUR][1000 genomes]
rs35856174	0.83[EUR][1000 genomes]
rs35941349	0.83[EUR][1000 genomes]
rs3786840	0.83[EUR][1000 genomes]
rs56946356	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60454376	0.83[EUR][1000 genomes]
rs62119101	0.83[EUR][1000 genomes]
rs62119102	0.83[EUR][1000 genomes]
rs62119103	0.83[EUR][1000 genomes]
rs62119105	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62119109	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62119116	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62120068	0.82[ASN][1000 genomes]
rs62121763	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62121764	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62121811	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121819	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121821	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62121823	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62121827	0.83[EUR][1000 genomes]
rs62121829	0.83[EUR][1000 genomes]
rs71356822	0.82[ASN][1000 genomes]
rs7246368	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248577	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7260070	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732135	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103530	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8104815	0.83[EUR][1000 genomes]
rs8105055	0.83[EUR][1000 genomes]
rs8105069	0.83[EUR][1000 genomes]
rs8105080	0.83[EUR][1000 genomes]
rs8105216	0.83[EUR][1000 genomes]
rs8105550	0.83[EUR][1000 genomes]
rs899199	0.83[EUR][1000 genomes]
rs899200	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12977238	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	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39143400-39154400	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr19:39143800-39153200	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr19:39144200-39153400	Genic enhancers	K562	blood
5	chr19:39144600-39154000	Enhancers	Right Atrium	heart
6	chr19:39144800-39154000	Genic enhancers	Fetal Intestine Large	intestine
7	chr19:39145200-39153400	Genic enhancers	Fetal Intestine Small	intestine
8	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:39147600-39154000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:39147600-39154000	Enhancers	Brain Angular Gyrus	brain
11	chr19:39147800-39160800	Enhancers	Placenta	Placenta
12	chr19:39148000-39152800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr19:39148600-39153400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
14	chr19:39148800-39153000	Weak transcription	Primary B cells from cord blood	blood
15	chr19:39149000-39154200	Enhancers	Brain Substantia Nigra	brain
16	chr19:39149000-39154600	Weak transcription	Primary T cells from cord blood	blood
17	chr19:39149000-39155200	Weak transcription	Fetal Brain Female	brain
18	chr19:39149200-39153400	Genic enhancers	Fetal Muscle Leg	muscle
19	chr19:39149400-39152600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr19:39149600-39153200	Weak transcription	Brain Germinal Matrix	brain
21	chr19:39149600-39154000	Enhancers	Brain Hippocampus Middle	brain
22	chr19:39149600-39160200	Enhancers	Pancreas	Pancrea
23	chr19:39150000-39153000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:39150000-39157600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
25	chr19:39150200-39152800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr19:39150200-39152800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr19:39150200-39154200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr19:39150400-39152600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:39150400-39152600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:39150400-39153200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:39150400-39153600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr19:39150400-39154400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:39150400-39155000	Genic enhancers	HMEC	breast
34	chr19:39150600-39152600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:39150600-39153000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr19:39150600-39154600	Genic enhancers	Osteobl	bone
37	chr19:39150800-39154400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:39150800-39155000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:39151000-39152600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr19:39151000-39154400	Genic enhancers	Muscle Satellite Cultured Cells	--
41	chr19:39151000-39154600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:39151200-39153000	Genic enhancers	Stomach Smooth Muscle	stomach
43	chr19:39151200-39153200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
44	chr19:39151200-39153200	Genic enhancers	NH-A	brain
45	chr19:39151200-39154800	Genic enhancers	HepG2	liver
46	chr19:39151200-39155800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr19:39151200-39157600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:39151200-39157600	Genic enhancers	Fetal Stomach	stomach
49	chr19:39151400-39152800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
50	chr19:39151400-39152800	Genic enhancers	Colon Smooth Muscle	Colon

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