Variant report

Variant	rs9836053
Chromosome Location	chr3:150885877-150885878
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150885743..150886838-chr3:151000415..151001396,8	K562	blood:
2	chr3:150885677..150886771-chr3:151000218..151001281,8	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1017348	0.89[CEU][hapmap]
rs10513387	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513393	0.88[CEU][hapmap]
rs1221002	1.00[ASW][hapmap];0.89[CEU][hapmap]
rs13321176	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs13322794	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388625	0.83[CEU][hapmap]
rs1549829	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554120	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17204437	0.88[CEU][hapmap]
rs17282940	0.83[CEU][hapmap]
rs17282947	0.88[CEU][hapmap]
rs17290219	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304673	1.00[ASN][1000 genomes]
rs1920393	1.00[ASN][1000 genomes]
rs1920397	0.89[CEU][hapmap]
rs2567325	0.83[CEU][hapmap]
rs6773020	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792089	0.94[CEU][hapmap]
rs722133	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155751	1.00[ASN][1000 genomes]
rs73155773	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155774	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7614811	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814936	0.88[CEU][hapmap]
rs9817216	0.88[CEU][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs9818251	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819885	0.88[CEU][hapmap]
rs9821749	1.00[ASN][1000 genomes]
rs9821937	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs9831242	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs9838990	0.88[CEU][hapmap]
rs9848789	0.88[CEU][hapmap]
rs9850762	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854017	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs9854126	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856118	0.83[CEU][hapmap]
rs9859854	0.88[CEU][hapmap]
rs9868643	0.87[CEU][hapmap]
rs9871229	1.00[ASN][1000 genomes]
rs9871624	1.00[CEU][hapmap]
rs9872645	0.88[CEU][hapmap]
rs9876268	0.94[CEU][hapmap]
rs9876933	0.88[CEU][hapmap]
rs9881116	0.94[CEU][hapmap];0.88[MEX][hapmap];1.00[ASN][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	nsv829756	chr3:150692636-150889738	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9836053	GYG1	cis	parietal	SCAN
rs9836053	MME	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150863200-150889000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:150865000-150886400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:150868800-150887400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:150871200-150888400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:150872800-150910800	Weak transcription	Brain Germinal Matrix	brain
6	chr3:150873200-150887000	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:150873200-150888800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:150873200-150910200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:150873600-150889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:150873800-150890000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:150873800-150890000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:150873800-150913800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:150874200-150888600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:150874200-150888800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:150874200-150896000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:150874600-150886200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:150874600-150888400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:150874600-150889200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:150874800-150900200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:150877600-150888800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:150878000-150888400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
23	chr3:150878400-150888800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:150878400-150890800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:150879000-150886200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:150879400-150886600	Weak transcription	Fetal Thymus	thymus
27	chr3:150879400-150887800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:150880400-150900200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:150880800-150900400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:150882800-150888200	Weak transcription	HepG2	liver
31	chr3:150883400-150889000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:150883800-150896000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:150884200-150887200	Weak transcription	Dnd41	blood
34	chr3:150884200-150888400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:150884200-150906600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:150884400-150893400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:150885800-150886200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:150885800-150887200	Enhancers	Primary neutrophils fromperipheralblood	blood

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