Variant report

Variant	rs7518199
Chromosome Location	chr1:154407419-154407420
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	chr1:154401123..154404227-chr1:154404483..154407452,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11265613	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12126142	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12133641	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12730036	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12730935	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12753254	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2228145	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4129267	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4133213	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4393147	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4453032	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4537545	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4576655	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845372	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845373	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845620	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845621	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845622	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845623	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56383622	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61812598	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6664201	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6684439	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512646	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7521458	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529229	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7518199	LINGO4	cis	parietal	SCAN
rs7518199	GPATCH4	cis	cerebellum	SCAN
rs7518199	NPR1	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154397000-154414200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:154399600-154409200	Enhancers	Placenta	Placenta
3	chr1:154400800-154410600	Strong transcription	Primary T cells from cord blood	blood
4	chr1:154402200-154407600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:154402400-154407800	Enhancers	Fetal Heart	heart
6	chr1:154403200-154408000	Enhancers	Right Ventricle	heart
7	chr1:154403200-154426000	Weak transcription	Brain Angular Gyrus	brain
8	chr1:154403800-154417600	Weak transcription	Small Intestine	intestine
9	chr1:154404200-154411400	Weak transcription	Fetal Kidney	kidney
10	chr1:154404400-154411400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:154404600-154412200	Weak transcription	A549	lung
12	chr1:154405200-154407600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
13	chr1:154405400-154407600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:154405400-154410600	Weak transcription	GM12878-XiMat	blood
15	chr1:154405400-154411600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:154405600-154409400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:154405600-154409800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:154405600-154411600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:154405600-154412200	Weak transcription	Psoas Muscle	Psoas
20	chr1:154405600-154413600	Weak transcription	Thymus	Thymus
21	chr1:154405800-154410600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:154405800-154410600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:154405800-154410800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:154405800-154411400	Weak transcription	HepG2	liver
25	chr1:154406000-154407600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:154406000-154408800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:154406000-154411400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:154406000-154412200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:154406000-154423200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:154406200-154407800	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:154406200-154408200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:154406200-154408400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:154406200-154408800	Strong transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:154406200-154410600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:154406200-154410800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:154406200-154411000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:154406200-154412600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:154406200-154417600	Weak transcription	Hela-S3	cervix
39	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
40	chr1:154406400-154410600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:154406400-154414000	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:154406600-154410400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:154406800-154407600	Active TSS	Colon Smooth Muscle	Colon
44	chr1:154406800-154407800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
45	chr1:154406800-154407800	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr1:154406800-154408400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:154406800-154408600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr1:154406800-154408800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:154406800-154409200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:154406800-154409400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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