Variant report

Variant	rs4672024
Chromosome Location	chr2:55377404-55377405
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55276124..55278386-chr2:55377199..55379824,2	MCF-7	breast:
2	chr2:55371026..55375430-chr2:55375600..55379751,6	K562	blood:
3	chr2:55366215..55370313-chr2:55376970..55382641,6	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11125556	0.83[CHB][hapmap]
rs1133181	0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1133182	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11679663	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11685292	0.83[ASN][1000 genomes]
rs12470651	0.83[CHB][hapmap]
rs12621144	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12990898	0.83[CHB][hapmap]
rs13012766	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs13013134	0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs13019355	0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs13021215	0.88[ASN][1000 genomes]
rs13023235	0.85[ASN][1000 genomes]
rs14026	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2576710	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs2864818	0.85[ASN][1000 genomes]
rs2920847	0.81[JPT][hapmap]
rs2920850	0.81[JPT][hapmap]
rs2920851	0.81[JPT][hapmap]
rs2968782	0.81[JPT][hapmap]
rs34564471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35026006	0.89[ASN][1000 genomes]
rs35161040	0.85[ASN][1000 genomes]
rs35890669	0.88[ASN][1000 genomes]
rs3762509	0.86[ASN][1000 genomes]
rs3935223	0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4420737	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4671241	0.92[ASN][1000 genomes]
rs4671242	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4672025	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs4672026	0.92[ASN][1000 genomes]
rs4672027	0.85[ASN][1000 genomes]
rs56095114	0.85[ASN][1000 genomes]
rs6545475	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs6545478	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs66483070	0.81[ASN][1000 genomes]
rs6714830	0.82[CHB][hapmap]
rs6715130	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs7595134	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7608118	0.83[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4672024	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs4672024	C2orf63	cis	cerebellum	SCAN
rs4672024	FLJ31438	cis	multi-tissue	Pritchard

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55361800-55378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:55365200-55381000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:55365600-55378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:55366200-55378600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:55367200-55378800	Weak transcription	Placenta	Placenta
6	chr2:55369800-55378200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:55369800-55378600	Weak transcription	Fetal Stomach	stomach
8	chr2:55370000-55379600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:55371600-55382400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:55373400-55381000	Weak transcription	Stomach Mucosa	stomach
11	chr2:55373800-55378600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:55374000-55378000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:55375200-55378400	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr2:55375800-55379600	Weak transcription	K562	blood
15	chr2:55376000-55378000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:55376000-55378400	Weak transcription	HSMMtube	muscle
17	chr2:55376000-55378400	Weak transcription	NHLF	lung
18	chr2:55376000-55378800	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:55376000-55378800	Weak transcription	Osteobl	bone
20	chr2:55376000-55379400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:55376000-55380400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:55376000-55381000	Weak transcription	Fetal Thymus	thymus
23	chr2:55376000-55381000	Weak transcription	HSMM	muscle
24	chr2:55376000-55383800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:55376200-55378800	Weak transcription	NHDF-Ad	bronchial
26	chr2:55376200-55379000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:55376200-55379200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:55376200-55379400	Weak transcription	NHEK	skin
29	chr2:55376400-55380800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:55376600-55378600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:55376800-55377600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:55376800-55378800	Weak transcription	Lung	lung
33	chr2:55376800-55382000	Enhancers	Primary B cells from peripheral blood	blood
34	chr2:55376800-55382400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr2:55377400-55378200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:55377400-55380200	Weak transcription	Hela-S3	cervix
37	chr2:55377400-55381800	Enhancers	GM12878-XiMat	blood
38	chr2:55377400-55382000	Enhancers	Primary B cells from cord blood	blood

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