Variant report

Variant	rs3843360
Chromosome Location	chr3:60041687-60041688
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11716199	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11718208	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs11718957	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720431	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11927585	0.84[ASN][1000 genomes]
rs13058814	0.84[CHB][hapmap];0.87[CHD][hapmap]
rs13062399	0.83[TSI][hapmap]
rs13063836	0.86[EUR][1000 genomes]
rs13066837	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs13069706	0.84[CHB][hapmap]
rs13070338	0.92[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs13075738	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17322850	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs17325451	0.83[CHB][hapmap]
rs2630166	0.87[ASN][1000 genomes]
rs35122656	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3845973	0.81[CEU][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs3856663	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs3856664	0.83[EUR][1000 genomes]
rs3856665	0.82[EUR][1000 genomes]
rs3856670	0.82[ASN][1000 genomes]
rs60458864	0.82[EUR][1000 genomes]
rs6779703	0.86[ASN][1000 genomes]
rs9311746	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3843360	SYNPR	cis	cerebellum	SCAN
rs3843360	FAM116A	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60034600-60044400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr3:60035000-60043200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr3:60035000-60043200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr3:60038000-60042800	Enhancers	Thymus	Thymus
5	chr3:60038200-60042800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr3:60038200-60043600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:60038600-60043000	Enhancers	Primary T cells from cord blood	blood
8	chr3:60039400-60043200	Enhancers	Fetal Thymus	thymus
9	chr3:60040800-60042800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:60040800-60042800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:60040800-60042800	Enhancers	Psoas Muscle	Psoas
12	chr3:60040800-60042800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr3:60041000-60043000	Enhancers	Fetal Heart	heart
14	chr3:60041000-60049000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:60041200-60042000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr3:60041200-60042000	Enhancers	NH-A	brain
17	chr3:60041200-60042200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:60041200-60042800	Enhancers	Fetal Muscle Leg	muscle
19	chr3:60041200-60043000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr3:60041400-60042000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:60041400-60042000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:60041400-60042000	Enhancers	Fetal Lung	lung
23	chr3:60041400-60042200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:60041400-60042200	Enhancers	NHEK	skin
25	chr3:60041400-60042400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:60041400-60042400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:60041600-60041800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:60041600-60041800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr3:60041600-60041800	Flanking Active TSS	Dnd41	blood
30	chr3:60041600-60042000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:60041600-60042000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:60041600-60042200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:60041600-60042400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:60041600-60042400	Enhancers	Fetal Stomach	stomach
35	chr3:60041600-60042600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:60041600-60042600	Enhancers	Brain Germinal Matrix	brain

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