Variant report

Variant	rs27016
Chromosome Location	chr5:179404008-179404009
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179402276..179404351-chr5:179406069..179408902,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10036834	0.81[CEU][hapmap]
rs10061480	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10068039	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10068529	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10068594	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10078977	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10479455	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10479557	0.82[EUR][1000 genomes]
rs10903246	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1102190	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1103811	0.84[GIH][hapmap]
rs12153541	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs12653944	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12656219	0.88[CHD][hapmap]
rs173562	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs185076	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs193718	0.87[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs248257	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248258	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248315	0.86[ASN][1000 genomes]
rs248316	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs248319	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs27013	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27014	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27017	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs27019	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28011	0.85[CHD][hapmap]
rs2937020	0.87[ASN][1000 genomes]
rs394588	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4130025	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs418384	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4340879	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4466125	0.80[EUR][1000 genomes]
rs449511	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700855	0.88[CHD][hapmap]
rs4700858	0.82[TSI][hapmap]
rs55734821	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62405021	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6871596	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6888883	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7706570	0.96[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs857181	0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs857182	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs857183	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs857184	0.85[ASN][1000 genomes]
rs857189	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs864137	0.87[ASN][1000 genomes]
rs864138	0.87[ASN][1000 genomes]
rs9329096	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][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
rs27016	TRIM7	cis	parietal	SCAN
rs27016	RASGEF1C	cis	cerebellum	SCAN

Chromatin state (count:107 , 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	chr5:179388800-179405000	Weak transcription	HUVEC	blood vessel
8	chr5:179388800-179405800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:179389000-179405800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:179389400-179411400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:179391800-179406200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:179392600-179414800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:179394400-179405200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:179395000-179405600	Weak transcription	Stomach Mucosa	stomach
15	chr5:179396600-179404200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:179396600-179461800	Weak transcription	HSMM	muscle
17	chr5:179399000-179406800	Strong transcription	Fetal Muscle Leg	muscle
18	chr5:179399000-179408000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:179399000-179408400	Strong transcription	Brain Germinal Matrix	brain
20	chr5:179399200-179405200	Strong transcription	Pancreas	Pancrea
21	chr5:179399200-179405800	Strong transcription	Adipose Nuclei	Adipose
22	chr5:179399200-179406800	Strong transcription	Fetal Stomach	stomach
23	chr5:179399400-179405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:179399400-179408000	Strong transcription	Left Ventricle	heart
25	chr5:179399400-179408200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr5:179399800-179408400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:179400000-179405000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:179400000-179405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:179400000-179408400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:179400000-179411400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:179400200-179406000	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:179400200-179407000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:179400200-179408200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:179400200-179408400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:179400400-179405200	Strong transcription	Fetal Intestine Small	intestine
36	chr5:179400400-179405800	Strong transcription	Right Ventricle	heart
37	chr5:179400400-179406600	Weak transcription	Dnd41	blood
38	chr5:179400400-179406800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr5:179400400-179407400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr5:179400400-179408000	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr5:179400400-179408400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:179400400-179412200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:179400600-179405200	Strong transcription	Placenta	Placenta
44	chr5:179400600-179405800	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr5:179400600-179408200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:179400600-179408200	Strong transcription	Lung	lung
47	chr5:179400600-179408400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:179400800-179405200	Strong transcription	Colon Smooth Muscle	Colon
49	chr5:179400800-179405800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:179400800-179405800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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