Variant report

Variant	rs9850440
Chromosome Location	chr3:53286688-53286689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53282491..53286758-chr3:53287434..53291520,6	K562	blood:
2	chr3:53283983..53288129-chr3:53288365..53291171,7	MCF-7	breast:
3	chr3:53282491..53286758-chr3:53287434..53291487,8	K562	blood:
4	chr3:53268931..53277907-chr3:53285563..53291617,11	MCF-7	breast:
5	chr3:53230450..53232412-chr3:53285677..53288510,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10433617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108506	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11551405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17030933	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030934	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17234092	1.00[CHB][hapmap]
rs17234771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235667	0.90[EUR][1000 genomes]
rs17306163	1.00[CHB][hapmap]
rs41275543	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56654807	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58558806	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59145995	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255989	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255993	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255994	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255999	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256000	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256003	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256009	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256043	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256049	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256050	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62256053	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256962	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256964	0.91[EUR][1000 genomes]
rs62256965	0.93[EUR][1000 genomes]
rs62256966	0.93[EUR][1000 genomes]
rs62256968	0.94[EUR][1000 genomes]
rs62256969	0.94[EUR][1000 genomes]
rs62257004	0.93[EUR][1000 genomes]
rs62257007	0.91[EUR][1000 genomes]
rs62257009	0.93[EUR][1000 genomes]
rs62257011	0.93[EUR][1000 genomes]
rs62257013	0.91[EUR][1000 genomes]
rs62257024	0.90[EUR][1000 genomes]
rs6780100	0.89[EUR][1000 genomes]
rs73080266	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080271	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080273	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080295	0.92[EUR][1000 genomes]
rs73082274	0.94[EUR][1000 genomes]
rs7622159	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9830594	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830895	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846315	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9864057	0.83[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes];0.90[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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9850440	TLR9	cis	parietal	SCAN
rs9850440	SFMBT1	cis	parietal	SCAN
rs9850440	PRKCD	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53272800-53288000	Weak transcription	Fetal Kidney	kidney
2	chr3:53276200-53287400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:53278600-53288000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:53278800-53287800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:53278800-53288200	Weak transcription	Psoas Muscle	Psoas
6	chr3:53280200-53288000	Weak transcription	Fetal Stomach	stomach
7	chr3:53280400-53288000	Weak transcription	Fetal Brain Female	brain
8	chr3:53280600-53288000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:53281400-53288000	Enhancers	Primary B cells from peripheral blood	blood
10	chr3:53281600-53288000	Enhancers	Thymus	Thymus
11	chr3:53281600-53288400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr3:53281800-53286800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:53281800-53287800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:53281800-53288000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:53281800-53288600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:53282000-53288000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr3:53282200-53287200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:53282400-53288000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:53282600-53286800	Weak transcription	Colonic Mucosa	Colon
20	chr3:53282600-53289600	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr3:53282800-53287600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:53283200-53288200	Enhancers	Pancreas	Pancrea
23	chr3:53283200-53288400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr3:53283400-53288200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr3:53283400-53288400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:53283600-53287800	Enhancers	Lung	lung
27	chr3:53283600-53288000	Enhancers	Brain Hippocampus Middle	brain
28	chr3:53283600-53288600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:53283600-53289600	Transcr. at gene 5' and 3'	A549	lung
30	chr3:53283800-53287000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:53284000-53286800	Enhancers	Brain Anterior Caudate	brain
32	chr3:53284000-53287200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:53284000-53287200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:53284000-53287200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:53284000-53288000	Enhancers	Colon Smooth Muscle	Colon
36	chr3:53284200-53288000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:53284400-53288000	Enhancers	Brain Substantia Nigra	brain
38	chr3:53284600-53287200	Genic enhancers	HMEC	breast
39	chr3:53284800-53287800	Enhancers	Osteobl	bone
40	chr3:53284800-53288000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:53285000-53287800	Enhancers	Brain Cingulate Gyrus	brain
42	chr3:53285000-53288000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:53285000-53288000	Enhancers	Stomach Mucosa	stomach
44	chr3:53285000-53288200	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr3:53285000-53288200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:53285000-53288600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr3:53285000-53289600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:53285200-53286800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:53285200-53286800	Enhancers	Fetal Lung	lung
50	chr3:53285200-53287800	Genic enhancers	Dnd41	blood

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