Variant report

Variant	rs1046263
Chromosome Location	chr2:47301744-47301745
allele	C/T
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47212859..47216615-chr2:47301507..47304672,4	MCF-7	breast:
2	chr2:47295023..47298657-chr2:47300855..47310213,9	MCF-7	breast:
3	chr2:47299662..47307017-chr2:47401146..47405423,11	MCF-7	breast:
4	chr2:47293721..47296795-chr2:47297396..47301843,4	K562	blood:
5	chr2:47301037..47304852-chr2:47397378..47400468,3	MCF-7	breast:
6	chr2:47298364..47306534-chr2:47399903..47404660,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALM2-3	chr2:47301452-47301966	ucscGeneNc_uc002rvu_1

No data

Variant related genes	Relation type
ENSG00000225187	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1046267	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1573958	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1807327	0.81[CEU][hapmap]
rs1807328	0.81[CEU][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap]
rs2692216	0.88[GIH][hapmap]
rs4952864	0.82[ASN][1000 genomes]
rs4953457	0.82[ASN][1000 genomes]
rs4953458	1.00[JPT][hapmap]
rs4953459	0.93[EUR][1000 genomes]
rs6544954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs736147	0.81[AMR][1000 genomes]
rs736148	0.81[AMR][1000 genomes]
rs7569495	0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs940737	0.87[GIH][hapmap]
rs9973596	1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1046263	SOCS5	cis	parietal	SCAN
rs1046263	FOXN2	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47292600-47302200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:47296000-47302000	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr2:47296200-47302200	Genic enhancers	Primary B cells from cord blood	blood
5	chr2:47297000-47303000	Genic enhancers	A549	lung
6	chr2:47297600-47302800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:47297800-47303400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:47297800-47303600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:47298000-47303000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:47298000-47303400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:47298000-47304400	Genic enhancers	Spleen	Spleen
12	chr2:47298800-47302400	Genic enhancers	Placenta	Placenta
13	chr2:47298800-47302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:47298800-47303000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:47298800-47303200	Enhancers	Fetal Brain Male	brain
16	chr2:47298800-47305200	Strong transcription	Thymus	Thymus
17	chr2:47299000-47303000	Weak transcription	Hela-S3	cervix
18	chr2:47299000-47303400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:47299200-47301800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:47299200-47304800	Strong transcription	Primary T cells from cord blood	blood
21	chr2:47299200-47306000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:47299400-47301800	Genic enhancers	Colonic Mucosa	Colon
23	chr2:47299400-47302000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:47299400-47302600	Weak transcription	HMEC	breast
25	chr2:47299400-47303800	Genic enhancers	Stomach Smooth Muscle	stomach
26	chr2:47299600-47302200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:47299600-47302400	Weak transcription	HUVEC	blood vessel
28	chr2:47299600-47303200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:47299600-47303200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:47299600-47303200	Genic enhancers	Placenta Amnion	Placenta Amnion
31	chr2:47299800-47302600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:47299800-47302600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr2:47299800-47303200	Genic enhancers	Fetal Muscle Leg	muscle
34	chr2:47299800-47303600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:47300000-47302200	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr2:47300000-47302600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:47300000-47302800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:47300200-47301800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:47300200-47302000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:47300200-47302200	Genic enhancers	Lung	lung
41	chr2:47300200-47302600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:47300200-47302800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:47300200-47303600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:47300400-47301800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:47300400-47301800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:47300400-47301800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:47300400-47302000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:47300400-47302200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:47300400-47302400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:47300400-47302400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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