Variant report

Variant	rs1344260
Chromosome Location	chr4:87403617-87403618
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10516775	0.87[EUR][1000 genomes]
rs10516776	0.87[EUR][1000 genomes]
rs17011953	0.87[EUR][1000 genomes]
rs17011954	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17011956	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17011959	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17011962	0.87[EUR][1000 genomes]
rs17011965	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.87[EUR][1000 genomes]
rs17011966	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17011968	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17011978	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17011981	0.87[EUR][1000 genomes]
rs17011984	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17011985	0.87[EUR][1000 genomes]
rs17011988	0.87[EUR][1000 genomes]
rs17011994	0.87[EUR][1000 genomes]
rs17012007	0.87[EUR][1000 genomes]
rs17012009	0.87[EUR][1000 genomes]
rs17012010	0.87[EUR][1000 genomes]
rs17012012	0.87[EUR][1000 genomes]
rs17012018	0.87[EUR][1000 genomes]
rs17419783	0.87[EUR][1000 genomes]
rs2170427	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2200052	0.87[EUR][1000 genomes]
rs2219993	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs28653505	0.90[EUR][1000 genomes]
rs2869442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2869443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2904103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34155193	0.87[EUR][1000 genomes]
rs35434858	0.87[EUR][1000 genomes]
rs4561893	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4604024	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4627823	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61121590	0.87[EUR][1000 genomes]
rs61344492	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72870675	0.87[EUR][1000 genomes]
rs72872208	0.87[EUR][1000 genomes]
rs72872209	0.87[EUR][1000 genomes]
rs7690137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980637	0.87[EUR][1000 genomes]
rs980638	0.90[EUR][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	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	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1344260	GPM6A	trans	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87394200-87405600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:87400200-87404200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:87400800-87403800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:87400800-87406800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:87401400-87405800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr4:87401600-87404200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:87402200-87403800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:87402200-87404000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:87402200-87404200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:87402200-87405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:87402400-87404800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:87402600-87404800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:87402800-87403800	Enhancers	Brain Cingulate Gyrus	brain
14	chr4:87402800-87404000	Enhancers	Fetal Lung	lung
15	chr4:87403400-87404000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr4:87403400-87404000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:87403400-87404200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr4:87403400-87404200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr4:87403400-87404200	Enhancers	Brain Germinal Matrix	brain
20	chr4:87403400-87404400	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr4:87403400-87404800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:87403400-87407200	Enhancers	Dnd41	blood
23	chr4:87403600-87403800	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr4:87403600-87403800	Flanking Active TSS	Fetal Brain Female	brain
25	chr4:87403600-87404000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr4:87403600-87404000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr4:87403600-87404000	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr4:87403600-87404000	Flanking Active TSS	Brain Substantia Nigra	brain
29	chr4:87403600-87404000	Enhancers	Colon Smooth Muscle	Colon
30	chr4:87403600-87404000	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr4:87403600-87404000	Enhancers	Fetal Brain Male	brain
32	chr4:87403600-87404200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr4:87403600-87404200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:87403600-87404200	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr4:87403600-87404200	Enhancers	Fetal Stomach	stomach
36	chr4:87403600-87404600	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr4:87403600-87405000	Enhancers	Fetal Kidney	kidney
38	chr4:87403600-87406200	Enhancers	Fetal Thymus	thymus

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