Variant report

Variant	rs27018
Chromosome Location	chr5:179405144-179405145
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	chr5:179404319..179405843-chr5:179497809..179500320,2	K562	blood:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10903246	0.81[GIH][hapmap]
rs1102191	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1103811	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12519642	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12653944	0.81[GIH][hapmap]
rs12654148	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12656814	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13161895	1.00[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13166286	0.92[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs13179406	0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17079966	1.00[CEU][hapmap];0.94[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];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17079968	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248318	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248320	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27012	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34027780	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34603792	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34674199	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35135297	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35592104	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35608303	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35973843	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35988237	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3719	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs379655	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797763	1.00[CEU][hapmap];0.94[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];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797764	1.00[CEU][hapmap];0.94[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];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs394616	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4129403	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4130025	0.81[GIH][hapmap]
rs4235504	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs438050	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4389651	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs442181	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700853	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs594202	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62405016	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6873781	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6873994	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6876648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71613437	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71613438	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs857187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs857188	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs863231	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs864481	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs864482	1.00[CEU][hapmap];0.94[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];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs27018	RNF130	cis	parietal	SCAN
rs27018	LMAN2	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179376600-179406600	Weak transcription	Psoas Muscle	Psoas
2	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
3	chr5:179381000-179407800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:179381200-179405600	Weak transcription	NHLF	lung
5	chr5:179381600-179411800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:179383200-179408600	Weak transcription	A549	lung
7	chr5:179388800-179405800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr5:179389000-179405800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:179389400-179411400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:179391800-179406200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:179392600-179414800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:179394400-179405200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:179395000-179405600	Weak transcription	Stomach Mucosa	stomach
14	chr5:179396600-179461800	Weak transcription	HSMM	muscle
15	chr5:179399000-179406800	Strong transcription	Fetal Muscle Leg	muscle
16	chr5:179399000-179408000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:179399000-179408400	Strong transcription	Brain Germinal Matrix	brain
18	chr5:179399200-179405200	Strong transcription	Pancreas	Pancrea
19	chr5:179399200-179405800	Strong transcription	Adipose Nuclei	Adipose
20	chr5:179399200-179406800	Strong transcription	Fetal Stomach	stomach
21	chr5:179399400-179405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:179399400-179408000	Strong transcription	Left Ventricle	heart
23	chr5:179399400-179408200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:179399800-179408400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:179400000-179405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:179400000-179408400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:179400000-179411400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:179400200-179406000	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:179400200-179407000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:179400200-179408200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:179400200-179408400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:179400400-179405200	Strong transcription	Fetal Intestine Small	intestine
33	chr5:179400400-179405800	Strong transcription	Right Ventricle	heart
34	chr5:179400400-179406600	Weak transcription	Dnd41	blood
35	chr5:179400400-179406800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr5:179400400-179407400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr5:179400400-179408000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr5:179400400-179408400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:179400400-179412200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr5:179400600-179405200	Strong transcription	Placenta	Placenta
41	chr5:179400600-179405800	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr5:179400600-179408200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:179400600-179408200	Strong transcription	Lung	lung
44	chr5:179400600-179408400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:179400800-179405200	Strong transcription	Colon Smooth Muscle	Colon
46	chr5:179400800-179405800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:179400800-179405800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr5:179400800-179407200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:179400800-179408000	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:179400800-179408000	Strong transcription	Duodenum Smooth Muscle	Duodenum

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