Variant report

Variant	rs6578414
Chromosome Location	chr11:3838489-3838490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3838017..3840276-chr11:3860830..3863822,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STIM1-1	chr11:3837982-3839379	ENSG00000250404.1

Variant related genes	Relation type
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1049388	1.00[ASN][1000 genomes]
rs11029983	1.00[ASN][1000 genomes]
rs11030043	1.00[ASN][1000 genomes]
rs11030044	1.00[ASN][1000 genomes]
rs11030055	1.00[ASN][1000 genomes]
rs11030173	1.00[ASN][1000 genomes]
rs11600857	1.00[ASN][1000 genomes]
rs11606318	1.00[ASN][1000 genomes]
rs11606483	1.00[ASN][1000 genomes]
rs17173882	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191448	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276405	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276453	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910577	1.00[ASN][1000 genomes]
rs4910846	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910852	1.00[ASN][1000 genomes]
rs4910856	1.00[ASN][1000 genomes]
rs4910857	1.00[ASN][1000 genomes]
rs61896929	1.00[ASN][1000 genomes]
rs61896930	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896931	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896953	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896954	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896956	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896957	1.00[ASN][1000 genomes]
rs61896958	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896959	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899361	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899362	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899363	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899392	1.00[ASN][1000 genomes]
rs61899393	1.00[ASN][1000 genomes]
rs7101788	1.00[ASN][1000 genomes]
rs72844340	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844341	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430467	1.00[ASN][1000 genomes]
rs74050940	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1038220	chr11:3818041-3860024	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1044882	chr11:3828986-3860024	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1044360	chr11:3832288-3860024	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6578414	STIM1	cis	parietal	SCAN
rs6578414	TSPAN32	cis	parietal	SCAN
rs6578414	IFITM3	cis	cerebellum	SCAN
rs6578414	OR52E2	cis	cerebellum	SCAN
rs6578414	OR56B1	cis	cerebellum	SCAN
rs6578414	CYB5R2	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3830200-3845200	Weak transcription	Spleen	Spleen
2	chr11:3830200-3845400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr11:3830200-3852400	Weak transcription	Fetal Brain Male	brain
4	chr11:3830400-3844600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:3830400-3844600	Weak transcription	Brain Germinal Matrix	brain
6	chr11:3830400-3844600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:3830400-3844600	Weak transcription	Thymus	Thymus
8	chr11:3830400-3845000	Weak transcription	Fetal Brain Female	brain
9	chr11:3830400-3846800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:3830400-3847200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:3830600-3844600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:3830600-3844800	Weak transcription	NHLF	lung
13	chr11:3830600-3845000	Weak transcription	GM12878-XiMat	blood
14	chr11:3830600-3845200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:3830600-3845600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:3830600-3847000	Weak transcription	Colonic Mucosa	Colon
17	chr11:3830600-3848000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:3830600-3861000	Weak transcription	Fetal Kidney	kidney
19	chr11:3830800-3838600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:3830800-3844000	Weak transcription	Brain Angular Gyrus	brain
21	chr11:3830800-3844400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:3830800-3844800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr11:3830800-3845200	Weak transcription	Pancreas	Pancrea
24	chr11:3830800-3845400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:3830800-3845400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:3830800-3845600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:3830800-3845800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:3830800-3845800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:3830800-3846000	Weak transcription	A549	lung
30	chr11:3830800-3846200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr11:3830800-3846200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:3830800-3846200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:3830800-3846600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:3831000-3842000	Weak transcription	Liver	Liver
35	chr11:3831000-3844800	Weak transcription	Dnd41	blood
36	chr11:3831000-3845400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr11:3831000-3845400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr11:3831000-3845800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:3831000-3845800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr11:3831000-3845800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr11:3831000-3846200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr11:3831000-3847600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:3831200-3846200	Weak transcription	Hela-S3	cervix
44	chr11:3831200-3847800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:3831400-3846200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:3831600-3846200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:3831600-3847200	Weak transcription	HepG2	liver
48	chr11:3832000-3844600	Weak transcription	Esophagus	oesophagus
49	chr11:3832200-3841000	Weak transcription	NHEK	skin
50	chr11:3832400-3845600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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