Variant report

Variant	rs11719654
Chromosome Location	chr3:150103135-150103136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150101451..150104370-chr3:150105337..150109927,7	K562	blood:
2	chr3:150103049..150105345-chr3:150109294..150110988,2	MCF-7	breast:
3	chr3:150093950..150095964-chr3:150101199..150103384,2	K562	blood:
4	chr3:150101054..150103942-chr3:150125603..150131015,6	K562	blood:
5	chr3:150090383..150092393-chr3:150101374..150104090,2	K562	blood:
6	chr3:150093390..150097610-chr3:150100766..150105118,7	MCF-7	breast:
7	chr3:150101273..150104730-chr3:150121434..150128062,8	K562	blood:
8	chr3:150098184..150100046-chr3:150100500..150103295,2	K562	blood:
9	chr3:150102544..150105170-chr3:150106754..150108675,2	K562	blood:
10	chr3:150101805..150104730-chr3:150121434..150125041,3	K562	blood:
11	chr3:150103102..150105201-chr3:150113061..150115315,2	K562	blood:
12	chr3:150101832..150103393-chr3:150130176..150133046,2	MCF-7	breast:
13	chr3:150100542..150102255-chr3:150102482..150105071,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11706784	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719816	1.00[JPT][hapmap]
rs12054166	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs12639090	0.86[YRI][hapmap]
rs13069723	0.88[ASN][1000 genomes]
rs13092207	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092341	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13097358	0.91[MEX][hapmap]
rs16862623	0.84[CEU][hapmap]
rs16862648	1.00[CHD][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs2068659	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28517277	0.81[ASN][1000 genomes]
rs33988810	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34192407	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34384576	0.88[ASN][1000 genomes]
rs34518530	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34616287	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34991086	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35704634	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35725711	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35982655	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56040746	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62269065	0.88[ASN][1000 genomes]
rs6440677	0.82[MEX][hapmap]
rs6763024	0.84[ASN][1000 genomes]
rs9682043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11719654	GPR149	cis	parietal	SCAN
rs11719654	TSC22D2	cis	cerebellum	SCAN
rs11719654	RAP2B	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150090200-150124600	Weak transcription	Aorta	Aorta
2	chr3:150090800-150107000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:150090800-150108600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:150090800-150111000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:150090800-150111000	Weak transcription	NHEK	skin
6	chr3:150094600-150106200	Weak transcription	HSMM	muscle
7	chr3:150094600-150108800	Weak transcription	NHLF	lung
8	chr3:150094800-150108200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:150096000-150105200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:150096200-150108400	Weak transcription	A549	lung
11	chr3:150097600-150103400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:150097800-150111200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:150102000-150103600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr3:150102200-150103400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:150102200-150103600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:150102200-150103600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:150102200-150103600	Enhancers	Placenta	Placenta
18	chr3:150102200-150103800	Enhancers	Fetal Thymus	thymus
19	chr3:150102400-150103200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:150102400-150103200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr3:150102400-150103200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr3:150102400-150103200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr3:150102400-150103200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr3:150102400-150103200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr3:150102400-150103200	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr3:150102400-150103200	Enhancers	Fetal Heart	heart
27	chr3:150102400-150103400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr3:150102400-150103400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:150102400-150103400	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr3:150102400-150103400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr3:150102400-150103400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:150102400-150103600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:150102400-150104000	Flanking Active TSS	GM12878-XiMat	blood
34	chr3:150102600-150103200	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr3:150102600-150103200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr3:150102600-150103200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:150102600-150103400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:150102600-150103400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:150102600-150103600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr3:150102600-150103600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr3:150102800-150103200	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr3:150102800-150103200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr3:150102800-150103400	Weak transcription	Left Ventricle	heart
44	chr3:150102800-150103400	Enhancers	HepG2	liver
45	chr3:150102800-150103600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr3:150102800-150103600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:150102800-150103600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:150102800-150103600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:150102800-150103800	Enhancers	H9 Cell Line	embryonic stem cell
50	chr3:150102800-150103800	Enhancers	Primary B cells from cord blood	blood

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