Variant report

Variant	rs3797567
Chromosome Location	chr5:115223035-115223036
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115175799..115178442-chr5:115221185..115223278,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145782	Chromatin interaction
ENSG00000177879	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10039749	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10050876	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10075784	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10751460	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11241336	0.95[ASN][1000 genomes]
rs11241337	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12188972	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12332653	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12513891	0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs12514553	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12517882	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12519850	0.94[ASN][1000 genomes]
rs12520442	0.94[ASN][1000 genomes]
rs12523122	0.94[ASN][1000 genomes]
rs13157716	0.95[ASN][1000 genomes]
rs13179199	0.93[ASN][1000 genomes]
rs13361489	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs152368	0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs152369	0.92[ASN][1000 genomes]
rs152397	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs152398	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs171809	0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2080902	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26529	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs26536	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs26537	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs26538	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs35238578	0.95[ASN][1000 genomes]
rs35501287	0.94[ASN][1000 genomes]
rs3733902	0.89[ASW][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3756555	0.85[CHB][hapmap]
rs3797564	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.82[ASN][1000 genomes]
rs3797565	0.93[ASN][1000 genomes]
rs3797566	0.85[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.80[ASN][1000 genomes]
rs3797568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797569	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs41332950	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4143542	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs58463583	0.82[ASN][1000 genomes]
rs59750231	0.95[ASN][1000 genomes]
rs61381571	0.94[ASN][1000 genomes]
rs6879485	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6880372	0.93[ASN][1000 genomes]
rs71581217	0.94[ASN][1000 genomes]
rs7707539	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7708164	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7713314	0.94[ASN][1000 genomes]
rs7723291	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv3401617	chr5:115205732-115238678	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv3368162	chr5:115205767-115230833	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv515611	chr5:115208843-115428381	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1021968	chr5:115213162-115426468	Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1024008	chr5:115222974-115431050	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1027117	chr5:115222974-115442883	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	esv2763487	chr5:115222986-115442895	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3797567	FEM1C	cis	parietal	SCAN
rs3797567	CDO1	cis	cerebellum	SCAN
rs3797567	ATG12	cis	lymphoblastoid	seeQTL
rs3797567	TRIM36	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115189800-115235800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr5:115193200-115239000	Weak transcription	Gastric	stomach
3	chr5:115193600-115234600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:115195400-115263200	Weak transcription	Aorta	Aorta
5	chr5:115196000-115233600	Weak transcription	Esophagus	oesophagus
6	chr5:115203400-115233400	Weak transcription	Fetal Brain Male	brain
7	chr5:115205600-115254200	Weak transcription	Small Intestine	intestine
8	chr5:115207600-115233600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:115207600-115238400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr5:115207600-115239200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:115207600-115244600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr5:115207600-115253800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:115207600-115254600	Weak transcription	Fetal Kidney	kidney
14	chr5:115207800-115227400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:115207800-115250800	Weak transcription	Adipose Nuclei	Adipose
16	chr5:115207800-115254000	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:115208000-115229200	Weak transcription	Primary B cells from cord blood	blood
18	chr5:115208000-115253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:115208200-115236000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:115208600-115235600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr5:115209200-115234200	Weak transcription	HSMM	muscle
22	chr5:115209400-115231200	Weak transcription	NHDF-Ad	bronchial
23	chr5:115209400-115232600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:115209800-115234000	Weak transcription	HUVEC	blood vessel
25	chr5:115212000-115225200	Weak transcription	Brain Angular Gyrus	brain
26	chr5:115212000-115236000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:115212600-115238200	Weak transcription	Dnd41	blood
28	chr5:115217800-115234000	Weak transcription	GM12878-XiMat	blood
29	chr5:115218400-115223600	Weak transcription	Fetal Brain Female	brain
30	chr5:115218600-115253000	Weak transcription	Placenta	Placenta
31	chr5:115218800-115253600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr5:115219000-115227600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:115219000-115252800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:115219200-115224600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:115219200-115231000	Weak transcription	NH-A	brain
36	chr5:115219200-115233600	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:115219200-115234000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:115219200-115252800	Weak transcription	Pancreas	Pancrea
39	chr5:115219200-115253200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:115219400-115223200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:115219400-115224000	Weak transcription	Ovary	ovary
42	chr5:115219400-115224600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:115219400-115230200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:115219400-115231000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:115219400-115233600	Weak transcription	Primary T cells from cord blood	blood
46	chr5:115219400-115234000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr5:115219400-115234200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:115219400-115234200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:115219400-115234200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr5:115219400-115234400	Weak transcription	Left Ventricle	heart

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