Variant report

Variant	rs12619400
Chromosome Location	chr2:55458325-55458326
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55458112..55461105-chr2:55507986..55510921,3	MCF-7	breast:
2	chr2:54195792..54198215-chr2:55457941..55460893,2	K562	blood:
3	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
4	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
5	chr2:55458256..55461079-chr2:55494634..55496499,3	K562	blood:
6	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
7	chr2:55458156..55461118-chr2:55494163..55499368,6	MCF-7	breast:
8	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162997	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12616435	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13021215	0.80[ASN][1000 genomes]
rs2164714	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2576710	0.84[ASN][1000 genomes]
rs2576724	0.94[ASN][1000 genomes]
rs2864818	0.81[ASN][1000 genomes]
rs34054131	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35026006	0.81[ASN][1000 genomes]
rs35161040	0.84[ASN][1000 genomes]
rs35890669	0.80[ASN][1000 genomes]
rs3762509	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4420737	0.80[ASN][1000 genomes]
rs56095114	0.82[ASN][1000 genomes]
rs56339196	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6758504	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12619400	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55451000-55458400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:55451000-55458400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:55451000-55458400	Weak transcription	Aorta	Aorta
4	chr2:55451000-55458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:55451000-55458400	Weak transcription	Fetal Brain Female	brain
6	chr2:55451000-55458600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:55451000-55458600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:55451000-55458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:55451000-55458800	Weak transcription	Esophagus	oesophagus
10	chr2:55451000-55458800	Weak transcription	Stomach Mucosa	stomach
11	chr2:55451200-55458400	Weak transcription	Fetal Kidney	kidney
12	chr2:55451200-55458400	Weak transcription	Fetal Lung	lung
13	chr2:55451400-55458400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:55451400-55458400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:55451400-55458600	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:55451400-55458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:55451800-55458400	Weak transcription	Brain Angular Gyrus	brain
18	chr2:55451800-55458600	Weak transcription	Fetal Intestine Small	intestine
19	chr2:55452200-55458600	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:55452400-55458400	Weak transcription	Fetal Stomach	stomach
21	chr2:55452600-55458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:55452600-55458400	Weak transcription	Brain Germinal Matrix	brain
23	chr2:55452800-55458400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:55453000-55458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:55453000-55458400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:55453000-55458600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:55453000-55458600	Weak transcription	Lung	lung
28	chr2:55453000-55458600	Weak transcription	Pancreas	Pancrea
29	chr2:55453000-55458800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:55453200-55458400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:55455000-55458400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr2:55455000-55458400	Enhancers	HepG2	liver
33	chr2:55455400-55458400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:55455600-55458400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:55455600-55458400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:55455600-55458600	Weak transcription	Adipose Nuclei	Adipose
37	chr2:55455600-55458600	Weak transcription	Brain Substantia Nigra	brain
38	chr2:55455800-55458400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:55455800-55458400	Weak transcription	Primary B cells from cord blood	blood
40	chr2:55455800-55458400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:55455800-55458400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:55455800-55458400	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:55455800-55458400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:55455800-55458400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:55455800-55458400	Weak transcription	GM12878-XiMat	blood
46	chr2:55455800-55458400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr2:55455800-55458600	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:55455800-55458600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:55455800-55458600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:55455800-55458800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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