Variant report

Variant	rs13224312
Chromosome Location	chr7:39688152-39688153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39686447..39688717-chr7:39690234..39692105,2	K562	blood:
2	chr7:39687898..39690458-chr7:39703472..39705888,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10232064	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10254562	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11769962	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11769987	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13240294	0.88[CEU][hapmap]
rs2008819	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2158547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2288743	0.88[CEU][hapmap]
rs2876856	0.88[CEU][hapmap]
rs35694450	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4723877	0.90[CEU][hapmap]
rs4723888	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6462938	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6462939	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6948088	0.95[ASN][1000 genomes]
rs7806633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7806769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13224312	PSMA2	cis	parietal	SCAN
rs13224312	C7orf11	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39666200-39694400	Weak transcription	Fetal Brain Female	brain
2	chr7:39667200-39698800	Weak transcription	Fetal Kidney	kidney
3	chr7:39671800-39693800	Weak transcription	A549	lung
4	chr7:39672200-39722800	Weak transcription	Hela-S3	cervix
5	chr7:39674000-39690200	Weak transcription	NH-A	brain
6	chr7:39674000-39690800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:39674200-39690000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:39674200-39691400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:39674200-39696000	Weak transcription	Thymus	Thymus
10	chr7:39675200-39708800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:39675600-39688200	Weak transcription	Fetal Stomach	stomach
12	chr7:39675600-39701400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr7:39675800-39691600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:39676600-39690200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:39676600-39694400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr7:39676600-39694400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:39676600-39694400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:39677400-39694200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr7:39678800-39694400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr7:39679600-39695800	Weak transcription	Primary B cells from cord blood	blood
21	chr7:39680000-39700800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:39680000-39701000	Weak transcription	Esophagus	oesophagus
23	chr7:39680000-39721600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr7:39680800-39689000	Weak transcription	NHDF-Ad	bronchial
25	chr7:39680800-39704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr7:39680800-39716400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:39682000-39700600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:39682000-39704000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr7:39682000-39704000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr7:39682400-39694400	Weak transcription	Fetal Intestine Large	intestine
31	chr7:39682400-39700600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:39682600-39688200	Weak transcription	Fetal Intestine Small	intestine
33	chr7:39682600-39696000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr7:39682600-39702600	Weak transcription	Gastric	stomach
35	chr7:39682800-39690200	Weak transcription	Stomach Mucosa	stomach
36	chr7:39682800-39722000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr7:39683400-39689800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:39683400-39701200	Weak transcription	Lung	lung
39	chr7:39683400-39716600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr7:39683600-39690200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr7:39683600-39696600	Weak transcription	Pancreas	Pancrea
42	chr7:39683600-39712600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:39684000-39690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr7:39684000-39694600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr7:39684400-39689800	Weak transcription	Osteobl	bone
46	chr7:39684600-39689000	Weak transcription	NHLF	lung
47	chr7:39684600-39690200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr7:39684600-39690400	Weak transcription	NHEK	skin
49	chr7:39685000-39689000	Weak transcription	HSMM	muscle
50	chr7:39685000-39689200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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