Variant report

Variant	rs6758504
Chromosome Location	chr2:55453099-55453100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55452459-55453201	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr2:55452841-55453104	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF1	chr2:55452729-55453123	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr2:55452687-55453176	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

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	chr2:55447082..55449248-chr2:55452286..55454032,2	MCF-7	breast:
4	chr2:55277719..55279534-chr2:55451997..55454923,2	K562	blood:
5	chr2:55452223..55454388-chr2:55835681..55838374,2	K562	blood:

No data

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

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12616435	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12619400	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13417057	0.84[ASN][1000 genomes]
rs2164714	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2576724	0.82[ASN][1000 genomes]
rs34054131	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3762509	0.85[EUR][1000 genomes]
rs56339196	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[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
rs6758504	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	chr2:55451000-55453800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr2:55451000-55454000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:55451000-55454200	Weak transcription	Primary B cells from cord blood	blood
4	chr2:55451000-55454200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:55451000-55454400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:55451000-55454800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:55451000-55454800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:55451000-55454800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:55451000-55454800	Weak transcription	HUVEC	blood vessel
10	chr2:55451000-55455000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:55451000-55455000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:55451000-55455000	Weak transcription	Fetal Intestine Large	intestine
13	chr2:55451000-55455000	Weak transcription	Right Atrium	heart
14	chr2:55451000-55455000	Weak transcription	Small Intestine	intestine
15	chr2:55451000-55455200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:55451000-55455200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:55451000-55455200	Weak transcription	Liver	Liver
18	chr2:55451000-55455200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:55451000-55455200	Weak transcription	Fetal Thymus	thymus
20	chr2:55451000-55455200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:55451000-55455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:55451000-55457200	Weak transcription	NHDF-Ad	bronchial
23	chr2:55451000-55457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:55451000-55457600	Weak transcription	HMEC	breast
25	chr2:55451000-55457800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:55451000-55457800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:55451000-55458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:55451000-55458000	Weak transcription	Osteobl	bone
29	chr2:55451000-55458400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:55451000-55458400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:55451000-55458400	Weak transcription	Aorta	Aorta
32	chr2:55451000-55458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:55451000-55458400	Weak transcription	Fetal Brain Female	brain
34	chr2:55451000-55458600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:55451000-55458600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:55451000-55458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:55451000-55458800	Weak transcription	Esophagus	oesophagus
38	chr2:55451000-55458800	Weak transcription	Stomach Mucosa	stomach
39	chr2:55451200-55453200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:55451200-55453800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:55451200-55454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:55451200-55454400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr2:55451200-55454400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr2:55451200-55454800	Weak transcription	Primary T cells from cord blood	blood
45	chr2:55451200-55454800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:55451200-55455000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:55451200-55455000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:55451200-55455000	Weak transcription	Brain Substantia Nigra	brain
49	chr2:55451200-55455200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:55451200-55458400	Weak transcription	Fetal Kidney	kidney

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