Variant report

Variant	rs34716955
Chromosome Location	chr4:73926670-73926671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1052080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721329	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727957	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11929937	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939939	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12500051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12507846	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13107336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13135799	0.84[ASN][1000 genomes]
rs13149759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13151642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17178078	0.85[ASN][1000 genomes]
rs1996057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs34230856	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762883	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62309635	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67424539	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6855349	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7442235	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973541	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949371	chr4:73678470-74094500	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv432611	chr4:73740665-74099265	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv998707	chr4:73753922-74044843	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv537136	chr4:73753922-74044843	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv917017	chr4:73754127-74044830	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1013174	chr4:73785324-74031884	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv537137	chr4:73785324-74031884	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1012068	chr4:73817769-74003079	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1014088	chr4:73817769-74031884	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv537138	chr4:73817769-74031884	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv533502	chr4:73819067-74044813	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	esv1849323	chr4:73926670-74115116	Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34716955	AFM	cis	parietal	SCAN
rs34716955	COX18	cis	parietal	SCAN
rs34716955	EREG	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73917200-73931000	Weak transcription	Fetal Heart	heart
2	chr4:73917200-73933800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:73917400-73932000	Weak transcription	Psoas Muscle	Psoas
4	chr4:73918600-73933000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr4:73918800-73930200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr4:73918800-73932200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:73918800-73933400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:73919000-73928600	Strong transcription	Fetal Intestine Large	intestine
9	chr4:73919000-73931400	Strong transcription	Liver	Liver
10	chr4:73919000-73932000	Strong transcription	Fetal Thymus	thymus
11	chr4:73919000-73932600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:73919000-73932800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:73919200-73928000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:73919200-73928200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:73919200-73930200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr4:73919200-73931200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr4:73919200-73931200	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:73919200-73932200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:73919400-73929200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:73919400-73929400	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:73919400-73930600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:73919600-73931600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr4:73920000-73928000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:73920200-73931400	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:73920400-73928200	Strong transcription	HSMM	muscle
26	chr4:73920400-73929600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr4:73920400-73930800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:73920600-73928000	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:73920600-73928000	Strong transcription	Osteobl	bone
30	chr4:73920600-73928200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:73920600-73930400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:73920600-73930600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:73920600-73930600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:73920600-73932400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:73920800-73930000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:73920800-73931400	Strong transcription	Dnd41	blood
37	chr4:73920800-73931800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr4:73920800-73934400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:73921000-73927200	Strong transcription	Left Ventricle	heart
40	chr4:73921000-73927400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr4:73921000-73928000	Strong transcription	Fetal Kidney	kidney
42	chr4:73921000-73928600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr4:73921000-73928800	Strong transcription	NH-A	brain
44	chr4:73921000-73931200	Strong transcription	Adipose Nuclei	Adipose
45	chr4:73921000-73931600	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr4:73921000-73933200	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:73921000-73933600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr4:73921200-73927600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr4:73921200-73927600	Strong transcription	HepG2	liver
50	chr4:73921200-73929800	Strong transcription	Fetal Lung	lung

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