Variant report

Variant	rs6549198
Chromosome Location	chr3:69362959-69362960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10865648	0.85[ASN][1000 genomes]
rs10865649	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs11707515	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12492029	0.83[ASN][1000 genomes]
rs12492475	0.85[ASN][1000 genomes]
rs1483895	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs17005615	0.84[ASN][1000 genomes]
rs1872152	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2007584	0.80[JPT][hapmap]
rs2170800	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs2314990	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2314992	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4428187	0.84[CHD][hapmap];0.80[JPT][hapmap]
rs4855308	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs4855389	0.83[CHD][hapmap];0.87[JPT][hapmap]
rs55728052	0.93[ASN][1000 genomes]
rs56119799	0.85[ASN][1000 genomes]
rs66686363	0.85[ASN][1000 genomes]
rs6776474	0.80[JPT][hapmap]
rs67846536	0.84[ASN][1000 genomes]
rs67940491	0.85[ASN][1000 genomes]
rs7627492	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7647743	0.84[ASN][1000 genomes]
rs7649373	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9833304	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9867480	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[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	nsv876935	chr3:69307942-69401248	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6549198	FRMD4B	cis	cerebellum	SCAN
rs6549198	PPP4R2	cis	parietal	SCAN
rs6549198	EBLN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69344000-69370000	Weak transcription	Fetal Brain Male	brain
2	chr3:69344000-69370000	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:69348000-69369400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:69349200-69368800	Weak transcription	Fetal Brain Female	brain
5	chr3:69350000-69374200	Weak transcription	Aorta	Aorta
6	chr3:69356000-69373200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:69356200-69368800	Weak transcription	Fetal Heart	heart
8	chr3:69356200-69369800	Weak transcription	Fetal Lung	lung
9	chr3:69356400-69371000	Weak transcription	Placenta	Placenta
10	chr3:69356400-69372000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:69357600-69366400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:69357800-69370000	Weak transcription	Spleen	Spleen
13	chr3:69358200-69370000	Weak transcription	Fetal Thymus	thymus
14	chr3:69358600-69369600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:69359400-69370000	Weak transcription	Thymus	Thymus
16	chr3:69359800-69363600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:69360200-69363600	Weak transcription	Brain Substantia Nigra	brain
18	chr3:69360600-69382200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:69360800-69372000	Weak transcription	HSMM	muscle
20	chr3:69361400-69372000	Weak transcription	HMEC	breast
21	chr3:69361800-69366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:69362000-69363000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr3:69362200-69363000	Strong transcription	NHEK	skin
24	chr3:69362600-69369400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:69362600-69370800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:69362600-69373200	Weak transcription	Dnd41	blood
27	chr3:69362800-69363600	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:69362800-69365400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:69362800-69366400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:69362800-69367600	Weak transcription	Lung	lung
31	chr3:69362800-69369400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:69362800-69369400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:69362800-69369600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:69362800-69369800	Weak transcription	HUVEC	blood vessel
35	chr3:69362800-69370200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:69362800-69371200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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