Variant report

Variant	rs7706943
Chromosome Location	chr5:96376766-96376767
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11740941	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11750003	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11958159	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs12109525	0.88[ASN][1000 genomes]
rs13161540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13165925	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13175726	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs172724	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs316206	0.83[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs316207	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[MEX][hapmap]
rs316208	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs316209	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs316211	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.99[ASN][1000 genomes]
rs316212	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316220	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs421173	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs445037	0.86[ASN][1000 genomes]
rs7720969	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7706943	CAST	cis	parietal	SCAN
rs7706943	LNPEP	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96351400-96379000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:96360600-96378600	Weak transcription	Gastric	stomach
3	chr5:96360800-96379400	Weak transcription	Psoas Muscle	Psoas
4	chr5:96361000-96378000	Weak transcription	Aorta	Aorta
5	chr5:96361800-96378800	Weak transcription	Fetal Heart	heart
6	chr5:96363400-96378000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:96364600-96383400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:96364800-96377600	Weak transcription	Fetal Kidney	kidney
9	chr5:96364800-96377800	Weak transcription	Fetal Lung	lung
10	chr5:96364800-96378000	Weak transcription	Pancreas	Pancrea
11	chr5:96364800-96378600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:96364800-96379400	Weak transcription	HUVEC	blood vessel
13	chr5:96364800-96379800	Weak transcription	Lung	lung
14	chr5:96364800-96380000	Weak transcription	Right Ventricle	heart
15	chr5:96364800-96382000	Weak transcription	NH-A	brain
16	chr5:96364800-96383000	Weak transcription	HMEC	breast
17	chr5:96365200-96377000	Weak transcription	K562	blood
18	chr5:96365600-96376800	Weak transcription	HSMM	muscle
19	chr5:96365800-96382000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:96367600-96379200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:96369800-96381800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:96370800-96380000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:96372400-96377600	Weak transcription	Primary B cells from cord blood	blood
24	chr5:96372400-96378600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:96372400-96378600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:96372400-96379400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:96372800-96381400	Weak transcription	Placenta	Placenta
28	chr5:96372800-96382600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:96373000-96379600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:96373200-96378800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:96373200-96382000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:96373600-96384600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr5:96373800-96378600	Weak transcription	Left Ventricle	heart
34	chr5:96374000-96377600	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:96374000-96378000	Weak transcription	Primary T cells from cord blood	blood
36	chr5:96374000-96378600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr5:96374000-96382000	Weak transcription	Dnd41	blood
38	chr5:96374400-96379200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr5:96374600-96384600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr5:96375000-96378600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:96375000-96378600	Weak transcription	Fetal Intestine Small	intestine
42	chr5:96375000-96379000	Weak transcription	HepG2	liver
43	chr5:96375000-96382000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:96375200-96378400	Weak transcription	Fetal Intestine Large	intestine

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