Variant report

Variant	rs152397
Chromosome Location	chr5:115188314-115188315
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	chr5:115176002..115179718-chr5:115188058..115191749,5	MCF-7	breast:
2	chr5:115187300..115190447-chr5:115192577..115195039,3	K562	blood:

Variant related genes	Relation type
ENSG00000177879	Chromatin interaction
ENSG00000145782	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10039749	0.94[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs10050876	0.86[ASN][1000 genomes]
rs1058600	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs10751460	0.96[ASN][1000 genomes]
rs11241336	0.97[ASN][1000 genomes]
rs11241337	0.82[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.96[ASN][1000 genomes]
rs12188972	1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12332653	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.95[ASN][1000 genomes]
rs12513891	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12514553	0.96[ASN][1000 genomes]
rs12517882	0.97[ASN][1000 genomes]
rs12519850	0.89[ASN][1000 genomes]
rs12520442	0.89[ASN][1000 genomes]
rs12523122	0.89[ASN][1000 genomes]
rs13157716	0.97[ASN][1000 genomes]
rs13179199	0.93[ASN][1000 genomes]
rs13361489	0.93[ASN][1000 genomes]
rs152368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs152369	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152398	0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs171809	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2080902	0.97[ASN][1000 genomes]
rs26529	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs26531	0.86[CHD][hapmap]
rs26533	0.80[ASN][1000 genomes]
rs26534	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs26535	0.81[ASN][1000 genomes]
rs26536	0.86[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs26537	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs26538	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.96[ASN][1000 genomes]
rs35179959	0.81[ASN][1000 genomes]
rs35238578	0.91[ASN][1000 genomes]
rs35501287	0.98[ASN][1000 genomes]
rs3733902	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3756555	0.81[CHB][hapmap];0.90[YRI][hapmap]
rs3797564	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap]
rs3797565	0.88[ASN][1000 genomes]
rs3797566	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap]
rs3797567	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs3797568	0.82[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.96[ASN][1000 genomes]
rs3797569	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3797570	0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs41332950	0.90[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4143542	1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs58463583	0.86[ASN][1000 genomes]
rs59750231	0.97[ASN][1000 genomes]
rs61381571	0.98[ASN][1000 genomes]
rs6872406	0.84[CHD][hapmap]
rs6879485	0.95[ASN][1000 genomes]
rs6880372	0.87[ASN][1000 genomes]
rs6880889	0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs71581217	0.89[ASN][1000 genomes]
rs7707539	0.96[ASN][1000 genomes]
rs7713314	0.98[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	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv3410990	chr5:115177597-115205832	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	esv3382194	chr5:115177673-115205801	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs152397	NCRNA00219	cis	cerebellum	SCAN
rs152397	ATG12	cis	lymphoblastoid	seeQTL
rs152397	ATG12	cis	multi-tissue	Pritchard

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115178600-115192200	Weak transcription	Gastric	stomach
2	chr5:115178800-115192200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:115179000-115189600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:115179000-115194800	Weak transcription	HSMMtube	muscle
5	chr5:115179400-115192200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:115179800-115193000	Weak transcription	Primary T cells from cord blood	blood
7	chr5:115179800-115205000	Weak transcription	HSMM	muscle
8	chr5:115180200-115192600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:115180200-115192600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:115180400-115189200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:115180600-115193000	Weak transcription	Fetal Stomach	stomach
12	chr5:115181400-115188800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:115181400-115189800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:115182000-115189000	Weak transcription	Primary B cells from cord blood	blood
15	chr5:115183400-115191000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:115183400-115193200	Weak transcription	HMEC	breast
17	chr5:115183400-115193400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:115183600-115192200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:115185400-115188800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:115185400-115195200	Weak transcription	Esophagus	oesophagus
21	chr5:115185600-115190800	Weak transcription	Right Ventricle	heart
22	chr5:115185600-115192200	Weak transcription	Left Ventricle	heart
23	chr5:115185600-115192200	Weak transcription	Pancreas	Pancrea
24	chr5:115185600-115192800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:115185600-115218600	Weak transcription	Lung	lung
26	chr5:115186400-115188400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:115186600-115189200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:115186800-115194000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:115187000-115192200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:115187000-115192200	Weak transcription	Liver	Liver
31	chr5:115187000-115192200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:115187000-115192600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr5:115187000-115193800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:115187200-115189200	Weak transcription	Fetal Intestine Large	intestine
35	chr5:115187200-115189400	Weak transcription	A549	lung
36	chr5:115187200-115189600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:115187200-115192000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:115187200-115192200	Weak transcription	Adipose Nuclei	Adipose
39	chr5:115187200-115192200	Weak transcription	Aorta	Aorta
40	chr5:115187200-115192200	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:115187200-115192400	Weak transcription	NHEK	skin
42	chr5:115187200-115192600	Weak transcription	Fetal Heart	heart
43	chr5:115187200-115192600	Weak transcription	Osteobl	bone
44	chr5:115187200-115206600	Weak transcription	Ovary	ovary
45	chr5:115187400-115192000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:115187400-115193600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:115187400-115206200	Weak transcription	Brain Hippocampus Middle	brain
48	chr5:115187600-115189600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:115187600-115191800	Weak transcription	Fetal Lung	lung
50	chr5:115187600-115192600	Weak transcription	Rectal Smooth Muscle	rectum

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