Variant report

Variant	rs301904
Chromosome Location	chr5:37111565-37111566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36876575..36878094-chr5:37110631..37112671,2	K562	blood:

Variant related genes	Relation type
ENSG00000164190	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10037834	0.82[EUR][1000 genomes]
rs10043395	0.83[EUR][1000 genomes]
rs10056009	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10056250	0.93[ASN][1000 genomes]
rs10057270	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];0.84[EUR][1000 genomes]
rs10068501	0.89[EUR][1000 genomes]
rs10069109	0.92[ASW][hapmap];0.88[CEU][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10072064	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10072288	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10076911	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10805625	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10941320	0.88[EUR][1000 genomes]
rs11958752	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12110010	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12110069	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12186733	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12515518	1.00[CEU][hapmap]
rs12518867	0.82[CEU][hapmap]
rs16903466	0.82[EUR][1000 genomes]
rs16903526	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16903578	1.00[CEU][hapmap]
rs2055129	1.00[CEU][hapmap]
rs2365910	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2365912	0.84[EUR][1000 genomes]
rs301861	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs301862	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs301864	0.87[EUR][1000 genomes]
rs301866	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs301868	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs301870	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[MKK][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs301871	0.89[EUR][1000 genomes]
rs301876	0.89[EUR][1000 genomes]
rs301877	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs301890	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301891	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.98[MKK][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs301892	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301893	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301894	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301895	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301902	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301903	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301907	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs301910	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs301911	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs301914	0.86[EUR][1000 genomes]
rs301915	0.86[EUR][1000 genomes]
rs301916	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3822471	0.86[CEU][hapmap]
rs6897283	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs73750950	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7724454	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9292649	0.85[EUR][1000 genomes]
rs9687825	1.00[CEU][hapmap]

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	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
12	nsv597823	chr5:37111565-37430365	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs301904	C9	cis	parietal	SCAN
rs301904	C6	cis	cerebellum	SCAN
rs301904	C5orf42	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37080200-37112000	Weak transcription	Fetal Heart	heart
2	chr5:37082800-37169200	Weak transcription	Spleen	Spleen
3	chr5:37087200-37113600	Weak transcription	NH-A	brain
4	chr5:37100800-37112000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:37101200-37115000	Weak transcription	A549	lung
6	chr5:37101400-37113400	Weak transcription	Brain Substantia Nigra	brain
7	chr5:37102200-37114400	Weak transcription	HMEC	breast
8	chr5:37102600-37115800	Strong transcription	HSMM	muscle
9	chr5:37102600-37121600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:37102800-37111600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:37102800-37112200	Weak transcription	HUVEC	blood vessel
12	chr5:37102800-37114200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:37103000-37113200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:37103600-37115800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:37103600-37135400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:37103800-37113600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:37103800-37143200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:37104800-37113400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:37105200-37119000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:37105400-37113200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:37105400-37113400	Weak transcription	Fetal Kidney	kidney
22	chr5:37105400-37114200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:37105400-37114800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:37105400-37120200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:37105400-37136400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:37105600-37111600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:37105800-37156200	Weak transcription	NHLF	lung
28	chr5:37106000-37143400	Weak transcription	HepG2	liver
29	chr5:37106200-37150200	Weak transcription	NHEK	skin
30	chr5:37107000-37115400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr5:37107000-37122000	Strong transcription	Fetal Muscle Leg	muscle
32	chr5:37107000-37122600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr5:37108000-37112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:37108200-37113200	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:37108200-37117800	Weak transcription	Esophagus	oesophagus
36	chr5:37108200-37143800	Weak transcription	Gastric	stomach
37	chr5:37108600-37111600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:37108600-37111600	Weak transcription	Fetal Brain Male	brain
39	chr5:37108600-37111600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:37108600-37112000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr5:37108600-37112600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:37108600-37113000	Weak transcription	Fetal Stomach	stomach
43	chr5:37108600-37113200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:37108600-37113400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:37108600-37113400	Weak transcription	Ovary	ovary
46	chr5:37108600-37113600	Weak transcription	Primary B cells from cord blood	blood
47	chr5:37108600-37117000	Weak transcription	Pancreas	Pancrea
48	chr5:37108600-37126400	Weak transcription	Lung	lung
49	chr5:37108600-37128200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr5:37108600-37139600	Weak transcription	Right Ventricle	heart

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