Variant report

Variant	rs34054131
Chromosome Location	chr2:55454763-55454764
allele	G/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	SPI1	chr2:55454758-55455646	HL-60	blood:	n/a	chr2:55455055-55455068 chr2:55455090-55455103 chr2:55455058-55455065
2	ZNF384	chr2:55454658-55455075	K562	blood:	n/a	n/a
3	TEAD4	chr2:55454738-55455785	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55450416..55452846-chr2:55452970..55454955,2	MCF-7	breast:
2	chr2:55120040..55122606-chr2:55452810..55455603,2	K562	blood:
3	chr2:55346562..55348270-chr2:55453778..55456492,2	K562	blood:
4	chr2:55277719..55279534-chr2:55451997..55454923,2	K562	blood:
5	chr2:55450659..55454031-chr2:55454419..55456893,3	K562	blood:

Variant related genes	Relation type
CLHC1	TF binding region
RPS27A	TF binding region
ENSG00000227799	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000162994	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1133181	0.83[ASN][1000 genomes]
rs1133182	0.83[ASN][1000 genomes]
rs11679663	0.83[ASN][1000 genomes]
rs11685292	0.80[AMR][1000 genomes]
rs12616435	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619400	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12621144	0.83[ASN][1000 genomes]
rs13012766	0.83[ASN][1000 genomes]
rs13013134	0.81[ASN][1000 genomes]
rs13019355	0.83[ASN][1000 genomes]
rs13021215	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13023235	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs14026	0.83[ASN][1000 genomes]
rs2164714	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2576710	0.84[ASN][1000 genomes]
rs2576724	0.94[ASN][1000 genomes]
rs2864818	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35026006	0.86[ASN][1000 genomes]
rs35161040	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35890669	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3762509	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3935223	0.82[ASN][1000 genomes]
rs4420737	0.85[ASN][1000 genomes]
rs4671241	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4671242	0.83[ASN][1000 genomes]
rs4672026	0.82[ASN][1000 genomes]
rs4672027	0.81[ASN][1000 genomes]
rs56095114	0.87[ASN][1000 genomes]
rs56339196	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545478	0.83[ASN][1000 genomes]
rs6758504	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7595134	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
rs34054131	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55451000-55454800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:55451000-55454800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:55451000-55454800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:55451000-55454800	Weak transcription	HUVEC	blood vessel
5	chr2:55451000-55455000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:55451000-55455000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:55451000-55455000	Weak transcription	Fetal Intestine Large	intestine
8	chr2:55451000-55455000	Weak transcription	Right Atrium	heart
9	chr2:55451000-55455000	Weak transcription	Small Intestine	intestine
10	chr2:55451000-55455200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:55451000-55455200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:55451000-55455200	Weak transcription	Liver	Liver
13	chr2:55451000-55455200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:55451000-55455200	Weak transcription	Fetal Thymus	thymus
15	chr2:55451000-55455200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:55451000-55455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:55451000-55457200	Weak transcription	NHDF-Ad	bronchial
18	chr2:55451000-55457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:55451000-55457600	Weak transcription	HMEC	breast
20	chr2:55451000-55457800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:55451000-55457800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:55451000-55458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:55451000-55458000	Weak transcription	Osteobl	bone
24	chr2:55451000-55458400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:55451000-55458400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:55451000-55458400	Weak transcription	Aorta	Aorta
27	chr2:55451000-55458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:55451000-55458400	Weak transcription	Fetal Brain Female	brain
29	chr2:55451000-55458600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:55451000-55458600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:55451000-55458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:55451000-55458800	Weak transcription	Esophagus	oesophagus
33	chr2:55451000-55458800	Weak transcription	Stomach Mucosa	stomach
34	chr2:55451200-55454800	Weak transcription	Primary T cells from cord blood	blood
35	chr2:55451200-55454800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:55451200-55455000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:55451200-55455000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:55451200-55455000	Weak transcription	Brain Substantia Nigra	brain
39	chr2:55451200-55455200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:55451200-55458400	Weak transcription	Fetal Kidney	kidney
41	chr2:55451200-55458400	Weak transcription	Fetal Lung	lung
42	chr2:55451400-55454800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:55451400-55455000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:55451400-55455000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:55451400-55455200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:55451400-55455200	Weak transcription	NHEK	skin
47	chr2:55451400-55455400	Weak transcription	Brain Anterior Caudate	brain
48	chr2:55451400-55455400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:55451400-55458400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:55451400-55458400	Weak transcription	Rectal Smooth Muscle	rectum

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