Variant report

Variant	rs7043984
Chromosome Location	chr9:95529408-95529409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr9:95529324-95530230	MCF-7	breast:	n/a	n/a
2	CTCF	chr9:95529340-95529490	MCF-7	breast:	n/a	n/a
3	POLR2A	chr9:95529311-95529450	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95494848..95496493-chr9:95528400..95531111,2	MCF-7	breast:
2	chr9:95423683..95425377-chr9:95528683..95530646,2	K562	blood:
3	chr9:95527312..95529710-chr9:95541794..95545254,3	K562	blood:
4	chr9:95086140..95089391-chr9:95526124..95530104,3	K562	blood:
5	chr9:95428069..95433526-chr9:95524054..95531235,7	MCF-7	breast:
6	chr9:95431564..95435112-chr9:95529358..95532432,3	K562	blood:
7	chr9:95431564..95435112-chr9:95528754..95531764,3	K562	blood:

No data

Variant related genes	Relation type
BICD2	TF binding region
ENSG00000188312	Chromatin interaction
ENSG00000198000	Chromatin interaction
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10114912	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10114932	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10118939	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10122383	0.95[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs10124058	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1022844	0.91[CEU][hapmap]
rs10491804	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs10761163	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10820994	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10821008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992366	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992393	0.91[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs10992424	0.94[EUR][1000 genomes]
rs10992450	0.92[EUR][1000 genomes]
rs10992457	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992471	0.87[ASN][1000 genomes]
rs13284106	0.87[EUR][1000 genomes]
rs13286566	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094281	0.82[AMR][1000 genomes]
rs2181585	0.81[CEU][hapmap]
rs2296669	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743875	0.91[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs4743876	0.94[EUR][1000 genomes]
rs4744137	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4744138	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4744141	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744143	0.89[EUR][1000 genomes]
rs6479431	0.93[EUR][1000 genomes]
rs7020104	0.91[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs7029939	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7046335	0.90[EUR][1000 genomes]
rs724102	0.87[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs747628	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs755209	0.94[EUR][1000 genomes]
rs7848399	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7852698	0.91[CEU][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs7861907	0.95[ASN][1000 genomes]
rs7864575	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7865019	0.82[AMR][1000 genomes]
rs7865118	0.89[EUR][1000 genomes]
rs7869521	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs7872610	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs987553	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430081	chr9:95502571-95568110	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7043984	OMD	cis	cerebellum	SCAN
rs7043984	CENPP	cis	cerebellum	SCAN
rs7043984	ZNF484	cis	cerebellum	SCAN
rs7043984	CENPP	cis	Esophagus Muscularis	GTEx
rs7043984	CENPP	cis	parietal	SCAN
rs7043984	ZNF484	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95528200-95529800	Weak transcription	Gastric	stomach
2	chr9:95528200-95532600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:95528200-95532600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:95528200-95533400	Enhancers	Stomach Mucosa	stomach
5	chr9:95528400-95530800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr9:95528400-95531800	Weak transcription	Primary T cells from cord blood	blood
7	chr9:95528400-95532400	Weak transcription	Psoas Muscle	Psoas
8	chr9:95528400-95532600	Weak transcription	Placenta	Placenta
9	chr9:95528600-95529800	Weak transcription	Colonic Mucosa	Colon
10	chr9:95528600-95529800	Weak transcription	Esophagus	oesophagus
11	chr9:95528600-95529800	Weak transcription	Pancreas	Pancrea
12	chr9:95528600-95529800	Weak transcription	Right Ventricle	heart
13	chr9:95528600-95530000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:95528600-95530400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:95528600-95531800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:95528600-95532200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr9:95528600-95532400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:95528600-95532400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:95528600-95532400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr9:95528600-95532400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:95528600-95532400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:95528600-95532600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:95528600-95532600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:95528600-95532600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:95528600-95532600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:95528600-95532600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:95528600-95532600	Weak transcription	Brain Anterior Caudate	brain
28	chr9:95528600-95532600	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:95528600-95532600	Weak transcription	Fetal Thymus	thymus
30	chr9:95528600-95532800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr9:95528600-95532800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:95528600-95532800	Weak transcription	Small Intestine	intestine
33	chr9:95528600-95533000	Weak transcription	Thymus	Thymus
34	chr9:95528800-95529800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:95528800-95529800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:95528800-95529800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:95528800-95529800	Weak transcription	Left Ventricle	heart
38	chr9:95528800-95529800	Weak transcription	Lung	lung
39	chr9:95528800-95529800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr9:95528800-95530400	Weak transcription	Fetal Heart	heart
41	chr9:95528800-95530600	Weak transcription	Right Atrium	heart
42	chr9:95528800-95530800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:95528800-95530800	Weak transcription	Fetal Intestine Large	intestine
44	chr9:95528800-95530800	Weak transcription	Spleen	Spleen
45	chr9:95528800-95530800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr9:95528800-95531000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr9:95528800-95531200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:95528800-95531600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr9:95528800-95531600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr9:95528800-95531600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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