Variant report

Variant	rs4672025
Chromosome Location	chr2:55384226-55384227
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	chr2:55275586..55279731-chr2:55383502..55386447,3	K562	blood:
2	chr2:55366338..55369324-chr2:55384110..55386041,3	K562	blood:
3	chr2:55378428..55381284-chr2:55382487..55384417,2	MCF-7	breast:
4	chr2:55384078..55385579-chr2:55388774..55390849,2	MCF-7	breast:
5	chr2:55366570..55369324-chr2:55383738..55386041,2	K562	blood:
6	chr2:18390509..18393280-chr2:55382468..55384962,2	MCF-7	breast:
7	chr2:55272933..55279731-chr2:55382949..55387132,8	K562	blood:
8	chr2:55275348..55277918-chr2:55382981..55385901,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10167669	0.81[ASN][1000 genomes]
rs11125555	0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11125556	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1133181	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs1133182	0.84[ASN][1000 genomes]
rs11679663	0.84[ASN][1000 genomes]
rs12470651	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621144	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs12623137	0.80[JPT][hapmap]
rs12990898	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13012766	0.84[ASN][1000 genomes]
rs13013134	0.82[ASN][1000 genomes]
rs13019355	0.84[ASN][1000 genomes]
rs14026	0.84[ASN][1000 genomes]
rs2576711	0.82[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs2576721	0.80[AMR][1000 genomes]
rs2589096	0.81[JPT][hapmap];0.95[MEX][hapmap]
rs34564471	0.83[ASN][1000 genomes]
rs35026006	0.80[ASN][1000 genomes]
rs3935223	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs4671241	0.84[ASN][1000 genomes]
rs4671242	0.84[ASN][1000 genomes]
rs4672024	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs4672026	0.84[ASN][1000 genomes]
rs6545475	0.82[CHB][hapmap]
rs6545478	0.84[ASN][1000 genomes]
rs66483070	0.92[ASN][1000 genomes]
rs6715130	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7595134	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs7608118	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4672025	CLHC1	cis	Artery Tibial	GTEx
rs4672025	VRK2	cis	parietal	SCAN
rs4672025	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs4672025	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs4672025	PRDXDD1P	cis	cerebellum	SCAN
rs4672025	CLHC1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55378000-55386800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:55378000-55386800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:55378200-55386200	Enhancers	Brain Hippocampus Middle	brain
4	chr2:55378200-55388000	Enhancers	Brain Cingulate Gyrus	brain
5	chr2:55378200-55388800	Enhancers	Adipose Nuclei	Adipose
6	chr2:55378600-55385600	Enhancers	Rectal Smooth Muscle	rectum
7	chr2:55378600-55386800	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr2:55378600-55386800	Enhancers	Fetal Stomach	stomach
9	chr2:55378800-55385600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:55378800-55386800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:55379200-55385200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:55379400-55385200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:55379400-55386600	Enhancers	Fetal Intestine Large	intestine
14	chr2:55379400-55387000	Enhancers	Fetal Intestine Small	intestine
15	chr2:55379600-55385000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:55379600-55386800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:55380000-55384400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:55380200-55386000	Enhancers	Hela-S3	cervix
19	chr2:55380400-55384400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:55380800-55385400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:55381000-55384400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr2:55381000-55387800	Enhancers	Fetal Muscle Leg	muscle
23	chr2:55381000-55391000	Enhancers	Stomach Mucosa	stomach
24	chr2:55381200-55390600	Enhancers	Brain Angular Gyrus	brain
25	chr2:55381400-55385600	Enhancers	Brain Germinal Matrix	brain
26	chr2:55381600-55386800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:55381600-55386800	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr2:55381800-55384400	Weak transcription	GM12878-XiMat	blood
29	chr2:55381800-55385200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:55381800-55385600	Enhancers	NHEK	skin
31	chr2:55381800-55387200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr2:55382000-55385000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:55382000-55385200	Enhancers	Fetal Lung	lung
34	chr2:55382000-55385400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:55382200-55384600	Weak transcription	Colonic Mucosa	Colon
36	chr2:55382200-55385400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:55382200-55385400	Bivalent Enhancer	HepG2	liver
38	chr2:55382400-55384800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:55382600-55385400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:55382600-55386200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:55383000-55384800	Enhancers	Psoas Muscle	Psoas
42	chr2:55383000-55385600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr2:55383000-55385800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr2:55383200-55385000	Enhancers	Ovary	ovary
45	chr2:55383400-55384400	Flanking Active TSS	HSMMtube	muscle
46	chr2:55383400-55384800	Enhancers	Right Ventricle	heart
47	chr2:55383400-55385000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:55383400-55385000	Enhancers	Fetal Brain Female	brain
49	chr2:55383400-55386600	Enhancers	Gastric	stomach
50	chr2:55383400-55386800	Enhancers	Left Ventricle	heart

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