Variant report

Variant	rs449511
Chromosome Location	chr5:179427400-179427401
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	chr5:179426841..179429316-chr5:179431530..179434128,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10036834	0.81[CEU][hapmap]
rs10061480	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs10068039	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10068529	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10068594	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10078977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10479455	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10479557	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10903246	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1102190	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1103811	0.84[GIH][hapmap]
rs12153541	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs12653944	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12656219	0.89[CHD][hapmap]
rs173562	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs185076	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs193718	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs248257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248315	0.91[ASN][1000 genomes]
rs248316	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248319	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27013	1.00[CEU][hapmap];0.95[CHB][hapmap];0.99[EUR][1000 genomes]
rs27014	1.00[CEU][hapmap];1.00[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]
rs27016	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]
rs27017	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs27019	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28011	0.85[CHD][hapmap]
rs2937020	0.89[ASN][1000 genomes]
rs394588	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4130025	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs418384	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4340879	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4466125	0.81[EUR][1000 genomes]
rs4700855	0.88[CHD][hapmap]
rs4700858	0.82[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs55734821	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62405021	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6871596	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6888883	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7706570	0.96[CEU][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs857181	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs857182	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857183	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs857184	0.90[ASN][1000 genomes]
rs857189	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs864137	0.89[ASN][1000 genomes]
rs864138	0.89[ASN][1000 genomes]
rs9329096	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.89[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs449511	TRIM7	cis	parietal	SCAN
rs449511	RASGEF1C	cis	parietal	SCAN
rs449511	RASGEF1C	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179404600-179439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:179405200-179428200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:179405200-179429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:179406000-179428600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:179407000-179428200	Weak transcription	Gastric	stomach
8	chr5:179408000-179427800	Weak transcription	Liver	Liver
9	chr5:179408000-179428200	Weak transcription	Left Ventricle	heart
10	chr5:179408200-179428000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:179416200-179428600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:179422000-179428800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:179422400-179429600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:179422600-179428000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:179422800-179428200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:179422800-179428600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:179423600-179428400	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:179423800-179428000	Weak transcription	Brain Substantia Nigra	brain
20	chr5:179423800-179428200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:179424000-179427800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:179424200-179428200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:179424600-179427400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:179425000-179428200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:179425000-179428400	Weak transcription	Spleen	Spleen
26	chr5:179425000-179439400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:179425200-179427800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:179425400-179428800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:179425600-179427800	Weak transcription	Placenta	Placenta
30	chr5:179425600-179428000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:179425600-179428000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:179425600-179428000	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:179425600-179428200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:179425600-179428600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:179425600-179428800	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:179425800-179428000	Weak transcription	Fetal Brain Male	brain
37	chr5:179425800-179428200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr5:179425800-179428200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:179425800-179428200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:179426000-179428200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:179426000-179428200	Weak transcription	HepG2	liver
42	chr5:179426000-179428400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:179426200-179428200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:179426200-179428200	Weak transcription	Ovary	ovary
45	chr5:179426200-179428800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:179426200-179440000	Weak transcription	Primary T cells from cord blood	blood
47	chr5:179426400-179428800	Weak transcription	Colonic Mucosa	Colon
48	chr5:179426400-179433400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:179426400-179438400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:179426400-179447200	Weak transcription	A549	lung

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