Variant report

Variant	rs6715130
Chromosome Location	chr2:55379420-55379421
allele	A/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	chr2:55378428..55381284-chr2:55382487..55384417,2	MCF-7	breast:
3	chr2:55371026..55375430-chr2:55375600..55379751,6	K562	blood:
4	chr2:55366215..55370313-chr2:55376970..55382641,6	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11125555	0.91[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11125556	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1133181	0.82[ASN][1000 genomes]
rs1133182	0.82[ASN][1000 genomes]
rs11679663	0.82[ASN][1000 genomes]
rs12470651	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12621144	0.82[ASN][1000 genomes]
rs12990898	0.84[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13012766	0.82[ASN][1000 genomes]
rs13019355	0.82[ASN][1000 genomes]
rs14026	0.82[ASN][1000 genomes]
rs2576711	0.82[JPT][hapmap];0.90[MEX][hapmap]
rs2589096	0.81[JPT][hapmap];0.90[MEX][hapmap]
rs34564471	0.86[ASN][1000 genomes]
rs3935223	0.81[ASN][1000 genomes]
rs4671241	0.82[ASN][1000 genomes]
rs4671242	0.82[ASN][1000 genomes]
rs4672024	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs4672025	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]
rs4672026	0.81[ASN][1000 genomes]
rs6545478	0.82[ASN][1000 genomes]
rs66483070	0.93[ASN][1000 genomes]
rs7595134	0.82[ASN][1000 genomes]
rs7608118	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.92[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6715130	VRK2	cis	parietal	SCAN
rs6715130	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs6715130	PRDXDD1P	cis	cerebellum	SCAN
rs6715130	FLJ31438	cis	multi-tissue	Pritchard
rs6715130	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs6715130	C2orf63	cis	cerebellum	SCAN
rs6715130	CLHC1	cis	Artery Tibial	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55365200-55381000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:55370000-55379600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:55371600-55382400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:55373400-55381000	Weak transcription	Stomach Mucosa	stomach
5	chr2:55375800-55379600	Weak transcription	K562	blood
6	chr2:55376000-55380400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:55376000-55381000	Weak transcription	Fetal Thymus	thymus
8	chr2:55376000-55381000	Weak transcription	HSMM	muscle
9	chr2:55376000-55383800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:55376400-55380800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:55376800-55382000	Enhancers	Primary B cells from peripheral blood	blood
12	chr2:55376800-55382400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:55377400-55380200	Weak transcription	Hela-S3	cervix
14	chr2:55377400-55381800	Enhancers	GM12878-XiMat	blood
15	chr2:55377400-55382000	Enhancers	Primary B cells from cord blood	blood
16	chr2:55377600-55381000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:55377600-55381800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr2:55378000-55386800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:55378000-55386800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:55378200-55380200	Enhancers	Brain Angular Gyrus	brain
21	chr2:55378200-55381000	Enhancers	Stomach Smooth Muscle	stomach
22	chr2:55378200-55382400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:55378200-55383600	Enhancers	Brain Substantia Nigra	brain
24	chr2:55378200-55386200	Enhancers	Brain Hippocampus Middle	brain
25	chr2:55378200-55388000	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:55378200-55388800	Enhancers	Adipose Nuclei	Adipose
27	chr2:55378400-55379800	Enhancers	HSMMtube	muscle
28	chr2:55378400-55381800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr2:55378400-55383800	Enhancers	NHLF	lung
30	chr2:55378600-55379800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:55378600-55383200	Enhancers	Colon Smooth Muscle	Colon
32	chr2:55378600-55383600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:55378600-55385600	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:55378600-55386800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr2:55378600-55386800	Enhancers	Fetal Stomach	stomach
36	chr2:55378800-55379600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:55378800-55379800	Enhancers	Lung	lung
38	chr2:55378800-55379800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:55378800-55380000	Enhancers	Fetal Muscle Leg	muscle
40	chr2:55378800-55380000	Enhancers	Osteobl	bone
41	chr2:55378800-55380200	Enhancers	Right Atrium	heart
42	chr2:55378800-55380800	Enhancers	Duodenum Mucosa	Duodenum
43	chr2:55378800-55382000	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr2:55378800-55382600	Enhancers	Placenta	Placenta
45	chr2:55378800-55383200	Enhancers	Fetal Brain Male	brain
46	chr2:55378800-55383600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:55378800-55385600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:55378800-55386800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:55379000-55379600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr2:55379000-55381000	Weak transcription	Esophagus	oesophagus

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