Variant report

Variant	rs12985403
Chromosome Location	chr19:39128967-39128968
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 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	chr19:39127442..39129054-chr19:39131156..39132692,2	MCF-7	breast:
9	chr19:39125934..39129387-chr19:39129539..39132887,4	MCF-7	breast:
10	chr19:39127191..39129568-chr19:39165594..39168572,2	K562	blood:
11	chr19:39126147..39129376-chr19:39327269..39331362,4	MCF-7	breast:
12	chr19:39126170..39130709-chr19:39210922..39213805,4	MCF-7	breast:
13	chr19:39127810..39130773-chr19:39133940..39135979,3	K562	blood:
14	chr19:39127732..39130687-chr19:39136486..39138250,3	MCF-7	breast:
15	chr19:39112082..39114534-chr19:39125989..39129017,3	MCF-7	breast:

No data

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

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12977252	0.86[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	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
rs12985403	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39111200-39130400	Strong transcription	Stomach Smooth Muscle	stomach
2	chr19:39111200-39130800	Strong transcription	Fetal Stomach	stomach
3	chr19:39111200-39131000	Weak transcription	Right Atrium	heart
4	chr19:39120800-39137800	Weak transcription	Fetal Brain Male	brain
5	chr19:39121600-39132400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:39123800-39132600	Weak transcription	Gastric	stomach
7	chr19:39123800-39137800	Weak transcription	Ovary	ovary
8	chr19:39125400-39129600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:39125600-39129600	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr19:39125800-39129000	Strong transcription	Adipose Nuclei	Adipose
11	chr19:39125800-39129800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:39125800-39129800	Strong transcription	Liver	Liver
13	chr19:39126000-39129000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:39126000-39129800	Strong transcription	Brain Germinal Matrix	brain
15	chr19:39126200-39129800	Strong transcription	Fetal Muscle Leg	muscle
16	chr19:39126200-39138200	Weak transcription	Psoas Muscle	Psoas
17	chr19:39126400-39138200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:39126600-39138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:39126800-39130000	Enhancers	HMEC	breast
20	chr19:39126800-39132400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:39126800-39136600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr19:39126800-39137800	Weak transcription	Brain Substantia Nigra	brain
23	chr19:39126800-39137800	Weak transcription	Fetal Lung	lung
24	chr19:39126800-39137800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:39127000-39131800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:39127000-39132600	Weak transcription	Colonic Mucosa	Colon
27	chr19:39127000-39137800	Weak transcription	Fetal Kidney	kidney
28	chr19:39127200-39135200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:39127400-39129400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr19:39127400-39129400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr19:39127400-39131600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:39127400-39132600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:39127400-39137800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:39127400-39137800	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:39127400-39137800	Weak transcription	Osteobl	bone
36	chr19:39127400-39138200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:39127600-39129000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:39127600-39129200	Weak transcription	Brain Anterior Caudate	brain
39	chr19:39127600-39129200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr19:39127600-39132600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr19:39127600-39137600	Weak transcription	Brain Angular Gyrus	brain
42	chr19:39127600-39137800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:39127600-39137800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:39127600-39137800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr19:39127600-39137800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:39127600-39137800	Weak transcription	Colon Smooth Muscle	Colon
47	chr19:39127600-39138200	Weak transcription	HSMM	muscle
48	chr19:39127600-39138400	Weak transcription	Aorta	Aorta
49	chr19:39127800-39129000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr19:39127800-39129200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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