Variant report

Variant	rs6755515
Chromosome Location	chr2:55452848-55452849
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 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	POLR2A	chr2:55452751-55452934	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:55452689-55452912	H1-hESC	embryonic stem cell:	n/a	n/a
6	TEAD4	chr2:55452709-55453066	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:55452643-55453017	H1-hESC	embryonic stem cell:	n/a	n/a
8	TEAD4	chr2:55452687-55453176	H1-hESC	embryonic stem cell:	n/a	n/a
9	USF2	chr2:55452835-55453038	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr2:55452712-55452936	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:55120040..55122606-chr2:55452810..55455603,2	K562	blood:
2	chr2:55447082..55449248-chr2:55452286..55454032,2	MCF-7	breast:
3	chr2:55277719..55279534-chr2:55451997..55454923,2	K562	blood:
4	chr2:55452223..55454388-chr2:55835681..55838374,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPS27A-2	chr2:55451842-55453044	NONHSAT070769

No data

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

Extended variants
information (count: 23 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10200120	0.87[ASN][1000 genomes]
rs1056445	0.83[ASN][1000 genomes]
rs11357	0.86[ASN][1000 genomes]
rs12052613	0.85[ASN][1000 genomes]
rs17852670	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2576712	0.85[ASN][1000 genomes]
rs2589080	0.86[ASN][1000 genomes]
rs2589092	0.80[ASN][1000 genomes]
rs2589093	0.83[ASN][1000 genomes]
rs2589100	0.84[ASN][1000 genomes]
rs2864819	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864826	0.85[ASN][1000 genomes]
rs2917779	0.87[ASN][1000 genomes]
rs2920967	0.85[ASN][1000 genomes]
rs4435493	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55997390	0.85[ASN][1000 genomes]
rs6545480	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6706815	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72799507	0.85[ASN][1000 genomes]
rs7597293	0.85[ASN][1000 genomes]
rs934709	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6755515	CLHC1	cis	Artery Aorta	GTEx
rs6755515	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs6755515	CLHC1	cis	Artery Tibial	GTEx
rs6755515	CLHC1	cis	Whole Blood	GTEx
rs6755515	CLHC1	cis	Nerve Tibial	GTEx
rs6755515	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs6755515	CLHC1	cis	Muscle Skeletal	GTEx
rs6755515	CLHC1	cis	Adipose Subcutaneous	GTEx
rs6755515	AC012358.7	cis	Adipose Subcutaneous	GTEx
rs6755515	CLHC1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55451000-55453000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:55451000-55453800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr2:55451000-55454000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:55451000-55454200	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55451000-55454200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:55451000-55454400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:55451000-55454800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:55451000-55454800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:55451000-55454800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:55451000-55454800	Weak transcription	HUVEC	blood vessel
11	chr2:55451000-55455000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:55451000-55455000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:55451000-55455000	Weak transcription	Fetal Intestine Large	intestine
14	chr2:55451000-55455000	Weak transcription	Right Atrium	heart
15	chr2:55451000-55455000	Weak transcription	Small Intestine	intestine
16	chr2:55451000-55455200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:55451000-55455200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:55451000-55455200	Weak transcription	Liver	Liver
19	chr2:55451000-55455200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:55451000-55455200	Weak transcription	Fetal Thymus	thymus
21	chr2:55451000-55455200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:55451000-55455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:55451000-55457200	Weak transcription	NHDF-Ad	bronchial
24	chr2:55451000-55457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:55451000-55457600	Weak transcription	HMEC	breast
26	chr2:55451000-55457800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:55451000-55457800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:55451000-55458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:55451000-55458000	Weak transcription	Osteobl	bone
30	chr2:55451000-55458400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:55451000-55458400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:55451000-55458400	Weak transcription	Aorta	Aorta
33	chr2:55451000-55458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:55451000-55458400	Weak transcription	Fetal Brain Female	brain
35	chr2:55451000-55458600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:55451000-55458600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:55451000-55458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:55451000-55458800	Weak transcription	Esophagus	oesophagus
39	chr2:55451000-55458800	Weak transcription	Stomach Mucosa	stomach
40	chr2:55451200-55453000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:55451200-55453000	Strong transcription	Dnd41	blood
42	chr2:55451200-55453200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:55451200-55453800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:55451200-55454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:55451200-55454400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:55451200-55454400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr2:55451200-55454800	Weak transcription	Primary T cells from cord blood	blood
48	chr2:55451200-55454800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:55451200-55455000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:55451200-55455000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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