Variant report

Variant	rs12977599
Chromosome Location	chr19:39139987-39139988
allele	A/G
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39138022..39142840-chr19:39322070..39325450,5	MCF-7	breast:
2	chr19:39138501..39140453-chr19:39331794..39333705,2	MCF-7	breast:
3	chr19:39137328..39141053-chr19:39337803..39340723,6	MCF-7	breast:
4	chr19:39137520..39139996-chr19:39320132..39324117,5	MCF-7	breast:
5	chr19:39135966..39142009-chr19:39184894..39201240,23	MCF-7	breast:
6	chr19:39107241..39111219-chr19:39136508..39140596,7	K562	blood:
7	chr19:39137047..39143767-chr19:39341076..39344906,12	MCF-7	breast:
8	chr19:39137584..39140325-chr19:39327324..39331607,4	MCF-7	breast:
9	chr19:39108167..39112213-chr19:39136508..39140596,7	K562	blood:
10	chr19:39138189..39142372-chr19:39210085..39214804,5	MCF-7	breast:
11	chr19:39139019..39141226-chr19:39211896..39214097,2	K562	blood:
12	chr19:39138420..39142103-chr19:39224990..39229224,5	MCF-7	breast:
13	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:
14	chr19:39104481..39107303-chr19:39137807..39140302,2	K562	blood:
15	chr19:39035426..39037334-chr19:39139289..39140832,2	K562	blood:
16	chr19:39138000..39140768-chr19:39215687..39223350,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267892	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1106372	0.80[AFR][1000 genomes]
rs12971309	0.80[AFR][1000 genomes]
rs12972997	0.80[AFR][1000 genomes]
rs12974733	0.80[AFR][1000 genomes]
rs12975079	0.80[AFR][1000 genomes]
rs12975256	0.80[AFR][1000 genomes]
rs12976598	0.80[AFR][1000 genomes]
rs12977238	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12978715	0.80[AFR][1000 genomes]
rs12978914	0.84[AFR][1000 genomes]
rs12980399	0.80[AFR][1000 genomes]
rs12981984	0.84[AFR][1000 genomes]
rs12985030	0.80[AFR][1000 genomes]
rs12985558	0.80[AFR][1000 genomes]
rs12986121	0.84[AFR][1000 genomes]
rs12986337	0.80[AFR][1000 genomes]
rs17589359	0.80[AFR][1000 genomes]
rs2086148	0.80[AFR][1000 genomes]
rs2126970	0.80[AFR][1000 genomes]
rs2279145	0.80[AFR][1000 genomes]
rs2279146	0.80[AFR][1000 genomes]
rs2287728	0.84[AFR][1000 genomes]
rs34026184	0.80[AFR][1000 genomes]
rs34082501	0.80[AFR][1000 genomes]
rs34083318	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34105297	0.88[AFR][1000 genomes]
rs34126343	0.92[AFR][1000 genomes]
rs34332511	0.80[AFR][1000 genomes]
rs34368672	0.88[AFR][1000 genomes]
rs34525537	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34558140	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34563817	0.80[AFR][1000 genomes]
rs34592527	0.92[AFR][1000 genomes]
rs34695688	0.87[ASN][1000 genomes]
rs34717167	0.80[AFR][1000 genomes]
rs34843929	0.81[AFR][1000 genomes]
rs34899634	0.80[AFR][1000 genomes]
rs35074956	0.92[AFR][1000 genomes]
rs35096737	0.80[AFR][1000 genomes]
rs35193699	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35281901	0.80[AFR][1000 genomes]
rs35436155	0.80[AFR][1000 genomes]
rs35488280	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35576862	0.80[AFR][1000 genomes]
rs35640008	0.80[AFR][1000 genomes]
rs35666464	0.80[AFR][1000 genomes]
rs35685980	0.92[AFR][1000 genomes]
rs35691365	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35716073	0.88[AFR][1000 genomes]
rs35729716	0.80[AFR][1000 genomes]
rs35807146	0.84[AFR][1000 genomes]
rs35856174	0.80[AFR][1000 genomes]
rs35941349	0.92[AFR][1000 genomes]
rs3786840	0.88[AFR][1000 genomes]
rs56946356	0.80[AFR][1000 genomes]
rs61121905	0.80[AFR][1000 genomes]
rs62119101	0.84[AFR][1000 genomes]
rs62119103	0.84[AFR][1000 genomes]
rs62119105	0.84[AFR][1000 genomes]
rs62119109	0.80[AFR][1000 genomes]
rs62119116	0.80[AFR][1000 genomes]
rs62120068	0.80[AFR][1000 genomes]
rs62121763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62121764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62121811	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121819	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62121821	0.80[ASN][1000 genomes]
rs62121823	0.92[AFR][1000 genomes]
rs62121827	0.85[AFR][1000 genomes]
rs62121828	0.88[AFR][1000 genomes]
rs62121829	0.85[AFR][1000 genomes]
rs71356822	0.80[AFR][1000 genomes]
rs7246368	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7260070	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103530	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8104815	0.80[AFR][1000 genomes]
rs8105055	0.80[AFR][1000 genomes]
rs8105069	0.80[AFR][1000 genomes]
rs8105080	0.80[AFR][1000 genomes]
rs8105216	0.80[AFR][1000 genomes]
rs8105550	0.80[AFR][1000 genomes]
rs899199	0.80[AFR][1000 genomes]
rs899200	0.80[AFR][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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv911667	chr19:39119898-39143289	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	esv18193	chr19:39138183-39140365	Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12977599	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39137600-39140400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:39137800-39140000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:39137800-39140000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:39137800-39140000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr19:39137800-39140000	Active TSS	Brain Substantia Nigra	brain
6	chr19:39137800-39140000	Active TSS	Fetal Lung	lung
7	chr19:39137800-39140000	Active TSS	Placenta	Placenta
8	chr19:39137800-39140000	Active TSS	Stomach Smooth Muscle	stomach
9	chr19:39137800-39140000	Active TSS	GM12878-XiMat	blood
10	chr19:39137800-39140000	Active TSS	K562	blood
11	chr19:39137800-39140200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr19:39137800-39140200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:39137800-39140200	Active TSS	Brain Angular Gyrus	brain
14	chr19:39137800-39140200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:39137800-39140200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr19:39137800-39140200	Active TSS	Ovary	ovary
17	chr19:39137800-39140200	Active TSS	Right Ventricle	heart
18	chr19:39137800-39140400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:39137800-39140600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr19:39137800-39140800	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr19:39137800-39140800	Active TSS	Rectal Smooth Muscle	rectum
22	chr19:39137800-39140800	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr19:39137800-39140800	Active TSS	NH-A	brain
24	chr19:39137800-39140800	Active TSS	NHDF-Ad	bronchial
25	chr19:39137800-39141200	Active TSS	Fetal Intestine Large	intestine
26	chr19:39137800-39141600	Active TSS	HSMMtube	muscle
27	chr19:39137800-39141800	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr19:39137800-39141800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr19:39138000-39140000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr19:39138000-39140000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:39138000-39140000	Active TSS	Brain Cingulate Gyrus	brain
32	chr19:39138000-39140000	Active TSS	Brain Hippocampus Middle	brain
33	chr19:39138000-39140000	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr19:39138000-39140200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:39138000-39140200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:39138000-39140200	Active TSS	NHEK	skin
37	chr19:39138000-39140400	Active TSS	HUVEC	blood vessel
38	chr19:39138000-39140400	Active TSS	Osteobl	bone
39	chr19:39138000-39140600	Active TSS	Hela-S3	cervix
40	chr19:39138000-39141000	Active TSS	NHLF	lung
41	chr19:39138000-39141200	Active TSS	Muscle Satellite Cultured Cells	--
42	chr19:39138000-39141200	Active TSS	Fetal Kidney	kidney
43	chr19:39138200-39140000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:39138200-39140000	Active TSS	Liver	Liver
45	chr19:39138200-39140200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:39138200-39140200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:39138200-39140200	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr19:39138200-39140200	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr19:39138200-39140200	Active TSS	Esophagus	oesophagus
50	chr19:39138200-39140200	Active TSS	Left Ventricle	heart

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