Variant report

Variant	rs4948089
Chromosome Location	chr7:55996162-55996163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10085802	0.82[ASN][1000 genomes]
rs10253539	0.82[ASN][1000 genomes]
rs10253680	0.82[ASN][1000 genomes]
rs12555	0.82[ASN][1000 genomes]
rs13223519	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13229704	0.82[ASN][1000 genomes]
rs13233834	0.82[ASN][1000 genomes]
rs13234504	0.82[ASN][1000 genomes]
rs13240361	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13241531	0.82[ASN][1000 genomes]
rs13247558	0.82[ASN][1000 genomes]
rs17151447	0.82[ASN][1000 genomes]
rs2304375	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2331184	0.82[ASN][1000 genomes]
rs33922584	0.82[ASN][1000 genomes]
rs34154824	0.82[ASN][1000 genomes]
rs34319969	0.82[ASN][1000 genomes]
rs34334997	0.82[ASN][1000 genomes]
rs34822782	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34885337	1.00[ASW][hapmap]
rs35007015	0.82[ASN][1000 genomes]
rs35058595	0.82[ASN][1000 genomes]
rs35136814	0.89[ASN][1000 genomes]
rs35347055	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs35506072	0.82[ASN][1000 genomes]
rs35515485	0.82[ASN][1000 genomes]
rs35523043	0.82[ASN][1000 genomes]
rs35581685	0.82[ASN][1000 genomes]
rs35881493	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs36044787	0.82[ASN][1000 genomes]
rs36049923	0.82[ASN][1000 genomes]
rs36148650	0.82[ASN][1000 genomes]
rs3778868	0.82[ASN][1000 genomes]
rs3816089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4307293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4947527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4947531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947532	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4948087	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4948101	0.89[ASN][1000 genomes]
rs71543775	0.89[ASN][1000 genomes]
rs71543776	0.85[ASN][1000 genomes]
rs71543777	0.89[ASN][1000 genomes]
rs73126344	0.82[ASN][1000 genomes]
rs816412	0.82[ASN][1000 genomes]
rs816413	0.82[ASN][1000 genomes]
rs816415	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv427782	chr7:55703073-56010314	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
8	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers 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	64 gene(s)	inside rSNPs	diseases
9	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
10	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
13	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv607034	chr7:55974028-56002247	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4948089	GBAS	cis	multi-tissue	Pritchard
rs4948089	Contig37142_RC	cis	multi-tissue	Pritchard

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:55955400-56004200	Weak transcription	Gastric	stomach
2	chr7:55956200-56002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:55956400-55998800	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:55969800-55998200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:55975000-56002000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:55975800-56006800	Weak transcription	Fetal Kidney	kidney
7	chr7:55977800-55997600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:55978800-55999400	Weak transcription	Placenta	Placenta
9	chr7:55980000-55999000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:55980000-56001400	Weak transcription	Spleen	Spleen
11	chr7:55980400-56004000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:55980600-55999400	Weak transcription	Psoas Muscle	Psoas
13	chr7:55980600-56001200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:55980600-56004200	Weak transcription	Right Ventricle	heart
15	chr7:55980800-55999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:55982600-56006200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:55984000-55998200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:55984800-55997000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:55985800-55999600	Weak transcription	Dnd41	blood
20	chr7:55986600-56006800	Weak transcription	Fetal Brain Male	brain
21	chr7:55988400-55996400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:55990200-55996200	Strong transcription	Brain Hippocampus Middle	brain
23	chr7:55990400-56000200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:55990600-55996400	Strong transcription	Fetal Lung	lung
25	chr7:55990800-55996200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:55990800-55996200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:55990800-55996600	Strong transcription	Fetal Brain Female	brain
28	chr7:55990800-55996800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr7:55991000-55998200	Weak transcription	Pancreas	Pancrea
30	chr7:55991400-56002200	Weak transcription	Aorta	Aorta
31	chr7:55991600-55996400	Weak transcription	Colonic Mucosa	Colon
32	chr7:55992200-55997800	Weak transcription	Adipose Nuclei	Adipose
33	chr7:55993000-56004200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr7:55993200-55998000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:55993400-56002200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr7:55993400-56002400	Weak transcription	Primary T cells from cord blood	blood
37	chr7:55993600-55997800	Weak transcription	Fetal Intestine Large	intestine
38	chr7:55993600-55999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:55993600-56001400	Weak transcription	Brain Substantia Nigra	brain
40	chr7:55993600-56001400	Weak transcription	HSMMtube	muscle
41	chr7:55993800-55999400	Weak transcription	Thymus	Thymus
42	chr7:55994000-55998200	Weak transcription	Fetal Intestine Small	intestine
43	chr7:55994200-55997400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:55994600-56000000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:55995200-55996200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr7:55995400-55996400	Strong transcription	Brain Anterior Caudate	brain
47	chr7:55995600-55996600	Strong transcription	Brain Germinal Matrix	brain
48	chr7:55995600-55996600	Strong transcription	Fetal Heart	heart
49	chr7:55995800-55996200	Strong transcription	Brain Angular Gyrus	brain
50	chr7:55995800-55996200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle

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