Variant report

Variant	rs12616435
Chromosome Location	chr2:55458080-55458081
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55457278-55458126	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:55458067-55458258	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54195792..54198215-chr2:55457941..55460893,2	K562	blood:
2	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
3	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:

Variant related genes	Relation type
RPS27A	TF binding region
ENSG00000170634	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1133181	0.82[ASN][1000 genomes]
rs1133182	0.82[ASN][1000 genomes]
rs11679663	0.82[ASN][1000 genomes]
rs11685292	0.80[AMR][1000 genomes]
rs12619400	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621144	0.82[ASN][1000 genomes]
rs13012766	0.82[ASN][1000 genomes]
rs13019355	0.82[ASN][1000 genomes]
rs13021215	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13023235	0.80[ASN][1000 genomes]
rs14026	0.82[ASN][1000 genomes]
rs2164714	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2576710	0.87[ASN][1000 genomes]
rs2576724	0.96[ASN][1000 genomes]
rs2864818	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34054131	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35026006	0.84[ASN][1000 genomes]
rs35161040	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35890669	0.83[ASN][1000 genomes]
rs3762509	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3935223	0.81[ASN][1000 genomes]
rs4420737	0.83[ASN][1000 genomes]
rs4671241	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4671242	0.82[ASN][1000 genomes]
rs4672026	0.81[ASN][1000 genomes]
rs56095114	0.85[ASN][1000 genomes]
rs56339196	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545478	0.82[ASN][1000 genomes]
rs6758504	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7595134	0.82[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
rs12616435	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 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	chr2:55455800-55458200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:55455800-55458400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:55455800-55458400	Weak transcription	Primary B cells from cord blood	blood
41	chr2:55455800-55458400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:55455800-55458400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:55455800-55458400	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:55455800-55458400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:55455800-55458400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr2:55455800-55458400	Weak transcription	GM12878-XiMat	blood
47	chr2:55455800-55458400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr2:55455800-55458600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:55455800-55458600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:55455800-55458600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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