Variant report

Variant	rs12977252
Chromosome Location	chr19:39128161-39128162
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39127830..39130773-chr19:39133940..39135979,2	K562	blood:
2	chr19:39016834..39019824-chr19:39127436..39129415,2	K562	blood:
3	chr19:39109649..39111361-chr19:39127209..39129073,2	MCF-7	breast:
4	chr19:39127720..39130630-chr19:39171842..39174626,3	MCF-7	breast:
5	chr19:39125533..39130601-chr19:39201644..39207054,6	MCF-7	breast:
6	chr19:39126407..39129417-chr19:39138116..39140606,3	MCF-7	breast:
7	chr19:39127496..39130057-chr19:39342762..39344272,2	MCF-7	breast:
8	chr19:39126238..39128898-chr19:39190173..39192471,2	K562	blood:
9	chr19:39127442..39129054-chr19:39131156..39132692,2	MCF-7	breast:
10	chr19:39125934..39129387-chr19:39129539..39132887,4	MCF-7	breast:
11	chr19:39127191..39129568-chr19:39165594..39168572,2	K562	blood:
12	chr19:39126429..39128678-chr19:39138239..39140432,2	K562	blood:
13	chr19:39126147..39129376-chr19:39327269..39331362,4	MCF-7	breast:
14	chr19:39126170..39130709-chr19:39210922..39213805,4	MCF-7	breast:
15	chr19:39127810..39130773-chr19:39133940..39135979,3	K562	blood:
16	chr19:39127732..39130687-chr19:39136486..39138250,3	MCF-7	breast:
17	chr19:39112082..39114534-chr19:39125989..39129017,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction
ENSG00000196218	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000269445	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12985403	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2232997	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2277941	0.84[AMR][1000 genomes];0.91[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12977252	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39111000-39128800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr19:39111200-39130400	Strong transcription	Stomach Smooth Muscle	stomach
3	chr19:39111200-39130800	Strong transcription	Fetal Stomach	stomach
4	chr19:39111200-39131000	Weak transcription	Right Atrium	heart
5	chr19:39120800-39137800	Weak transcription	Fetal Brain Male	brain
6	chr19:39121600-39132400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:39123800-39132600	Weak transcription	Gastric	stomach
8	chr19:39123800-39137800	Weak transcription	Ovary	ovary
9	chr19:39125200-39128200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr19:39125400-39128400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:39125400-39128400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:39125400-39128400	Genic enhancers	Fetal Intestine Small	intestine
13	chr19:39125400-39128400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
14	chr19:39125400-39128400	Genic enhancers	NHEK	skin
15	chr19:39125400-39128800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:39125400-39129600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:39125600-39128400	Genic enhancers	K562	blood
18	chr19:39125600-39129600	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr19:39125800-39129000	Strong transcription	Adipose Nuclei	Adipose
20	chr19:39125800-39129800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:39125800-39129800	Strong transcription	Liver	Liver
22	chr19:39126000-39129000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:39126000-39129800	Strong transcription	Brain Germinal Matrix	brain
24	chr19:39126200-39129800	Strong transcription	Fetal Muscle Leg	muscle
25	chr19:39126200-39138200	Weak transcription	Psoas Muscle	Psoas
26	chr19:39126400-39128400	Enhancers	Stomach Mucosa	stomach
27	chr19:39126400-39138200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:39126600-39128200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr19:39126600-39128800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:39126600-39138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:39126800-39130000	Enhancers	HMEC	breast
32	chr19:39126800-39132400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:39126800-39136600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr19:39126800-39137800	Weak transcription	Brain Substantia Nigra	brain
35	chr19:39126800-39137800	Weak transcription	Fetal Lung	lung
36	chr19:39126800-39137800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr19:39127000-39128400	Enhancers	Primary T cells fromperipheralblood	blood
38	chr19:39127000-39131800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:39127000-39132600	Weak transcription	Colonic Mucosa	Colon
40	chr19:39127000-39137800	Weak transcription	Fetal Kidney	kidney
41	chr19:39127200-39128400	Enhancers	Fetal Intestine Large	intestine
42	chr19:39127200-39135200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:39127400-39128200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr19:39127400-39128400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr19:39127400-39128400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr19:39127400-39128400	Enhancers	Hela-S3	cervix
47	chr19:39127400-39129400	Enhancers	H1 Cell Line	embryonic stem cell
48	chr19:39127400-39129400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:39127400-39131600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:39127400-39132600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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