Variant report

Variant	rs301907
Chromosome Location	chr5:37105095-37105096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10037834	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10043395	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10052880	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10056009	0.87[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10057270	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10068328	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10068501	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10069109	0.92[ASW][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10072064	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10072288	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[EUR][1000 genomes]
rs10076911	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10473043	0.82[MEX][hapmap]
rs10805625	0.87[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10941320	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11958752	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12108953	0.88[EUR][1000 genomes]
rs12110010	0.87[CEU][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12110069	1.00[EUR][1000 genomes]
rs12186733	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12515518	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12515522	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12515577	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12518867	0.82[CEU][hapmap]
rs12520562	0.85[EUR][1000 genomes]
rs16903477	0.85[EUR][1000 genomes]
rs16903526	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2055129	0.87[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2081109	0.86[EUR][1000 genomes]
rs2365910	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2366275	0.88[EUR][1000 genomes]
rs300052	0.84[ASN][1000 genomes]
rs301861	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301862	0.87[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs301864	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs301866	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301868	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs301870	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301871	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs301876	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301877	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301890	0.92[ASW][hapmap];0.87[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs301891	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs301892	0.92[ASW][hapmap];0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs301893	0.92[ASW][hapmap];0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs301894	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs301895	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs301902	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs301903	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs301904	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs301910	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301911	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301914	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301915	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301916	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3849756	0.85[EUR][1000 genomes]
rs6859227	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6897283	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73750950	0.97[EUR][1000 genomes]
rs7712984	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7724454	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9292649	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' 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	65 gene(s)	inside rSNPs	diseases
3	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv917880	chr5:36948778-37115342	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	esv1802391	chr5:36958598-37242600	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv597822	chr5:36997953-37147152	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv534064	chr5:37054962-37586210	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv964844	chr5:37080836-37107123	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv881511	chr5:37088627-37552852	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs301907	C5orf42	cis	cerebellum	SCAN
rs301907	C9	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37065000-37107600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:37067000-37111400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:37080200-37112000	Weak transcription	Fetal Heart	heart
4	chr5:37082000-37109000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:37082800-37169200	Weak transcription	Spleen	Spleen
6	chr5:37087000-37105200	Weak transcription	Lung	lung
7	chr5:37087000-37107000	Weak transcription	Pancreas	Pancrea
8	chr5:37087200-37106800	Weak transcription	Hela-S3	cervix
9	chr5:37087200-37113600	Weak transcription	NH-A	brain
10	chr5:37094200-37106400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:37097800-37107000	Weak transcription	Brain Angular Gyrus	brain
12	chr5:37099400-37107600	Weak transcription	Gastric	stomach
13	chr5:37100000-37106800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:37100800-37112000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:37101000-37107200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:37101200-37107600	Weak transcription	Right Ventricle	heart
17	chr5:37101200-37115000	Weak transcription	A549	lung
18	chr5:37101400-37113400	Weak transcription	Brain Substantia Nigra	brain
19	chr5:37102200-37107600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr5:37102200-37108000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:37102200-37114400	Weak transcription	HMEC	breast
22	chr5:37102400-37105400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:37102400-37105400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:37102400-37105600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:37102400-37105800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:37102600-37107600	Weak transcription	Psoas Muscle	Psoas
27	chr5:37102600-37109400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:37102600-37115800	Strong transcription	HSMM	muscle
29	chr5:37102600-37121600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:37102800-37107600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:37102800-37110800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:37102800-37111600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:37102800-37112200	Weak transcription	HUVEC	blood vessel
34	chr5:37102800-37114200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:37103000-37105600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:37103000-37106800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:37103000-37107400	Weak transcription	Brain Anterior Caudate	brain
38	chr5:37103000-37108600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr5:37103000-37109200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:37103000-37109400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:37103000-37110000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:37103000-37110000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:37103000-37113200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:37103200-37105400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:37103200-37105600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:37103200-37105600	Strong transcription	Brain Germinal Matrix	brain
47	chr5:37103200-37110000	Strong transcription	Adipose Nuclei	Adipose
48	chr5:37103400-37105400	Strong transcription	Fetal Kidney	kidney
49	chr5:37103400-37105400	Strong transcription	Left Ventricle	heart
50	chr5:37103400-37105400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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