Variant report

Variant	rs10941361
Chromosome Location	chr5:37695743-37695744
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10461983	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10461984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10805626	0.81[CHB][hapmap]
rs11749343	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11749345	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12513493	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12517792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519774	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12520294	0.91[ASN][1000 genomes]
rs12521092	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12656733	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs13154033	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159969	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13171010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13182520	0.90[ASN][1000 genomes]
rs13182737	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs13185923	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13187416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363925	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16903666	0.83[CHB][hapmap]
rs1862577	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1874178	0.83[CHB][hapmap]
rs2973086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4431371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs525463	0.83[CHB][hapmap]
rs581376	0.83[CHB][hapmap]
rs665327	0.83[CHB][hapmap]
rs677084	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs682825	0.83[CHB][hapmap]
rs6897494	0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs7700431	0.83[CHB][hapmap]
rs781794	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs870100	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs9292665	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10941361	RXFP3	cis	cerebellum	SCAN
rs10941361	GDNF	cis	cerebellum	SCAN
rs10941361	LIFR	cis	parietal	SCAN
rs10941361	LOC643787	cis	multi-tissue	Pritchard
rs10941361	SLC1A3	cis	parietal	SCAN
rs10941361	OXCT1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37682200-37698000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:37682800-37696000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:37683800-37696600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:37684400-37700000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:37684400-37705000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr5:37685000-37695800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:37685200-37696600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:37685200-37743200	Weak transcription	Gastric	stomach
9	chr5:37685400-37717600	Weak transcription	Pancreas	Pancrea
10	chr5:37685600-37711200	Weak transcription	Fetal Stomach	stomach
11	chr5:37685600-37727000	Weak transcription	Lung	lung
12	chr5:37687200-37720600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr5:37688400-37721400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:37688400-37721400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:37688400-37723600	Weak transcription	Placenta	Placenta
16	chr5:37689600-37696000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:37689600-37696600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:37689600-37726000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:37692200-37721200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:37693800-37705200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:37694000-37695800	Strong transcription	Primary T cells from cord blood	blood
22	chr5:37694600-37698400	Weak transcription	Dnd41	blood
23	chr5:37694800-37698400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:37694800-37698400	Weak transcription	Adipose Nuclei	Adipose
25	chr5:37695200-37716600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr5:37695400-37696800	Enhancers	Psoas Muscle	Psoas
27	chr5:37695400-37698000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr5:37695400-37698400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr5:37695400-37706000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr5:37695400-37715600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:37695400-37722600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr5:37695600-37697400	Enhancers	Hela-S3	cervix
33	chr5:37695600-37697400	Enhancers	HMEC	breast
34	chr5:37695600-37698200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:37695600-37698400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:37695600-37702000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr5:37695600-37703000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:37695600-37706400	Weak transcription	Liver	Liver
39	chr5:37695600-37721200	Weak transcription	Primary monocytes fromperipheralblood	blood

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