Variant report

Variant	rs17419929
Chromosome Location	chr4:87609320-87609321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10008165	0.84[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10023787	0.84[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10029671	0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs10030525	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10031843	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1021101	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1026861	0.83[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1035191	0.81[GIH][hapmap]
rs10516778	0.95[GIH][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap]
rs11097115	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11943428	0.85[ASN][1000 genomes]
rs11947018	0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1420621	0.83[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs1481833	0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17011986	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17419295	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17419627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17420607	0.95[GIH][hapmap];0.80[JPT][hapmap]
rs17453839	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454662	0.81[ASN][1000 genomes]
rs17694112	0.82[GIH][hapmap]
rs2006842	0.81[GIH][hapmap]
rs2054592	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2230600	0.83[TSI][hapmap]
rs2287147	0.82[GIH][hapmap]
rs28483710	0.85[ASN][1000 genomes]
rs28485273	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28529445	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28534599	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28535527	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28663376	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28678816	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28735881	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3775238	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs3775239	0.81[GIH][hapmap]
rs4277747	0.80[ASN][1000 genomes]
rs4513526	0.85[ASN][1000 genomes]
rs4529013	0.85[JPT][hapmap]
rs4693780	0.82[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap]
rs55640323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55654230	0.82[ASN][1000 genomes]
rs55746316	0.85[ASN][1000 genomes]
rs55757426	0.85[ASN][1000 genomes]
rs55773619	0.85[ASN][1000 genomes]
rs55879246	0.85[ASN][1000 genomes]
rs55978957	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56150118	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56178389	0.84[ASN][1000 genomes]
rs56296936	0.85[ASN][1000 genomes]
rs56348925	0.83[ASN][1000 genomes]
rs6531932	0.84[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs66669421	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67274037	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67341369	0.81[ASN][1000 genomes]
rs67523832	0.82[ASN][1000 genomes]
rs67928053	0.85[ASN][1000 genomes]
rs6838659	0.81[JPT][hapmap]
rs6847139	0.85[JPT][hapmap]
rs72665759	0.83[ASN][1000 genomes]
rs72665762	0.83[ASN][1000 genomes]
rs72665769	0.82[ASN][1000 genomes]
rs72665771	0.85[ASN][1000 genomes]
rs72665772	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72665777	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72665791	0.81[ASN][1000 genomes]
rs7694723	0.84[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9307020	0.88[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs969734	0.91[GIH][hapmap];0.80[JPT][hapmap]
rs9992507	0.89[MKK][hapmap]
rs9993042	0.89[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2755470	chr4:87536515-87613212	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17419929	LIN54	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87574600-87644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87579200-87642600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:87579400-87644400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:87579600-87611800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:87585200-87618000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:87586400-87643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:87591800-87639000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:87591800-87641000	Weak transcription	Brain Anterior Caudate	brain
9	chr4:87592400-87627800	Weak transcription	HMEC	breast
10	chr4:87592400-87656400	Weak transcription	Adipose Nuclei	Adipose
11	chr4:87592600-87620600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:87593800-87641400	Weak transcription	Brain Angular Gyrus	brain
13	chr4:87594400-87610400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:87594400-87642600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:87594400-87659800	Weak transcription	Ovary	ovary
16	chr4:87594600-87610200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:87594600-87610200	Weak transcription	Fetal Lung	lung
18	chr4:87594800-87622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:87594800-87639200	Weak transcription	Fetal Kidney	kidney
20	chr4:87595000-87610600	Weak transcription	NHDF-Ad	bronchial
21	chr4:87595200-87610200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:87595200-87638200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:87595200-87651200	Weak transcription	Fetal Stomach	stomach
24	chr4:87595400-87622800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:87597800-87610200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:87599000-87609400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:87600400-87610000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:87600400-87639200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:87601400-87610000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:87601400-87610600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:87601800-87615000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:87603600-87615200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:87604200-87622200	Weak transcription	Fetal Brain Male	brain
34	chr4:87604800-87638200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:87605000-87624800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:87605600-87610800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:87606400-87609400	Enhancers	NHEK	skin
38	chr4:87606400-87613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:87606600-87624800	Weak transcription	Esophagus	oesophagus
40	chr4:87606800-87610200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:87606800-87610200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:87606800-87612800	Weak transcription	Brain Substantia Nigra	brain
43	chr4:87606800-87613600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:87606800-87641000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:87607600-87616400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:87609000-87609600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:87609000-87609600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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