Variant report

Variant	rs7305016
Chromosome Location	chr12:51642543-51642544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51640501..51643365-chr12:51664040..51666792,2	K562	blood:
2	chr12:51638552..51640559-chr12:51641323..51644888,4	MCF-7	breast:
3	chr12:51608943..51615058-chr12:51635250..51642835,14	K562	blood:
4	chr12:51640991..51642656-chr12:51660376..51662126,2	K562	blood:

Variant related genes	Relation type
ENSG00000170545	Chromatin interaction
ENSG00000184271	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10735832	0.84[JPT][hapmap]
rs10783422	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783423	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783425	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876154	0.85[EUR][1000 genomes]
rs10876155	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169761	0.84[JPT][hapmap]
rs1130598	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3886185	0.85[LWK][hapmap]
rs3888223	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4761935	0.86[LWK][hapmap];0.85[MKK][hapmap]
rs6421171	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580809	0.92[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs6580816	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6580817	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7307217	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7309376	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7314235	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7398443	0.84[EUR][1000 genomes]
rs7959901	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[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	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	esv3324940	chr12:51640852-51648054	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7305016	LOC57228	cis	multi-tissue	Pritchard
rs7305016	SPATS2	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51635200-51647000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:51636200-51643200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:51636200-51657000	Weak transcription	Small Intestine	intestine
4	chr12:51638400-51653000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:51638400-51662800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:51639200-51642600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:51639200-51642800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:51639200-51644600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:51639400-51642600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:51639400-51642800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:51639400-51642800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:51639600-51642600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:51639800-51643000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:51639800-51643200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr12:51639800-51643600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:51639800-51646600	Weak transcription	Aorta	Aorta
17	chr12:51639800-51656800	Weak transcription	HSMMtube	muscle
18	chr12:51639800-51662800	Weak transcription	Fetal Stomach	stomach
19	chr12:51640000-51643200	Enhancers	Spleen	Spleen
20	chr12:51640000-51656400	Weak transcription	A549	lung
21	chr12:51640200-51642600	Enhancers	Primary B cells from peripheral blood	blood
22	chr12:51640200-51643200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:51640200-51656400	Weak transcription	Hela-S3	cervix
24	chr12:51640200-51662800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:51640200-51662800	Weak transcription	Pancreas	Pancrea
26	chr12:51640400-51643000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:51640400-51643400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:51640400-51651000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:51640400-51659000	Weak transcription	HMEC	breast
30	chr12:51640400-51661600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:51640600-51642600	Weak transcription	HSMM	muscle
32	chr12:51640600-51643000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr12:51640600-51649000	Weak transcription	NHEK	skin
34	chr12:51640600-51656600	Weak transcription	NHDF-Ad	bronchial
35	chr12:51640600-51661800	Weak transcription	NH-A	brain
36	chr12:51640800-51642600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr12:51640800-51642600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr12:51640800-51642800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr12:51640800-51643000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr12:51640800-51644800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr12:51641000-51642600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr12:51641000-51642600	Enhancers	Primary T cells from cord blood	blood
43	chr12:51641000-51656600	Weak transcription	Osteobl	bone
44	chr12:51641200-51643800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:51641600-51648400	Weak transcription	Fetal Intestine Small	intestine
46	chr12:51641600-51651000	Weak transcription	Fetal Intestine Large	intestine
47	chr12:51641600-51663000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:51641800-51643200	Strong transcription	Thymus	Thymus
49	chr12:51641800-51644000	Weak transcription	Brain Angular Gyrus	brain
50	chr12:51641800-51644400	Weak transcription	Muscle Satellite Cultured Cells	--

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