Variant report

Variant	rs1443360
Chromosome Location	chr9:92763466-92763467
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:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:92761640..92763658-chr9:92766942..92769443,2	MCF-7	breast:
2	chr9:92756890..92759147-chr9:92762216..92764609,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GADD45G-5	chr9:92763074-92763500	XLOC_007451
2	lnc-GADD45G-5	chr9:92762923-92763500	XLOC_007451
3	lnc-GADD45G-5	chr9:92762923-92763500	NONHSAT132983
4	lnc-GADD45G-5	chr9:92762923-92763500	NONHSAT132986

No data

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13296044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1373102	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1443358	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35150414	0.87[AMR][1000 genomes]
rs501675	0.87[AMR][1000 genomes]
rs535599	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs557789	0.88[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs601472	0.88[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs613212	0.87[AMR][1000 genomes]
rs627985	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs628020	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs633926	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs636460	0.81[AMR][1000 genomes]
rs650415	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs650882	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs661232	0.87[AMR][1000 genomes]
rs666603	0.87[AMR][1000 genomes]
rs679273	0.88[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs683669	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7018766	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7036231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704476	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs920752	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1443360	SEMA4D	cis	parietal	SCAN
rs1443360	SEMA4D	cis	cerebellum	SCAN
rs1443360	CKS2	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92753600-92765400	Enhancers	Fetal Intestine Large	intestine
2	chr9:92754000-92765400	Enhancers	Fetal Intestine Small	intestine
3	chr9:92757400-92770000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:92757600-92764200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:92757600-92770000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:92758800-92767600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:92760800-92766000	Enhancers	Fetal Brain Male	brain
8	chr9:92761200-92763600	Enhancers	Small Intestine	intestine
9	chr9:92761200-92765400	Enhancers	Fetal Thymus	thymus
10	chr9:92761200-92767400	Enhancers	Fetal Muscle Leg	muscle
11	chr9:92761600-92763600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:92761600-92763600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr9:92761600-92764600	Enhancers	Placenta	Placenta
14	chr9:92761600-92765200	Enhancers	Right Ventricle	heart
15	chr9:92761600-92765200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr9:92761600-92765600	Enhancers	Lung	lung
17	chr9:92761600-92765800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr9:92761600-92766400	Enhancers	Fetal Stomach	stomach
19	chr9:92761800-92763600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:92761800-92763800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:92761800-92763800	Enhancers	Fetal Brain Female	brain
22	chr9:92761800-92766600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr9:92762200-92764000	Weak transcription	Aorta	Aorta
24	chr9:92762400-92763600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:92762400-92763800	Enhancers	Brain Germinal Matrix	brain
26	chr9:92762400-92764000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:92762400-92764600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr9:92762400-92764600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:92762400-92764600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr9:92762400-92765400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:92762400-92766600	Enhancers	Colon Smooth Muscle	Colon
32	chr9:92762600-92763600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:92762600-92763600	Enhancers	Primary T cells from cord blood	blood
34	chr9:92762600-92763600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr9:92762600-92763600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr9:92762600-92763600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr9:92762600-92763600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr9:92762600-92763600	Enhancers	Adipose Nuclei	Adipose
39	chr9:92762600-92763600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr9:92762600-92763600	Enhancers	Fetal Kidney	kidney
41	chr9:92762600-92763600	Enhancers	NHDF-Ad	bronchial
42	chr9:92762600-92764200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:92762600-92764400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr9:92762600-92764600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:92762600-92764600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:92762600-92764600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:92762600-92764600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:92762600-92764600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:92762600-92765800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:92762600-92765800	Enhancers	Fetal Lung	lung

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