Variant report

Variant	rs1400280
Chromosome Location	chr12:39241240-39241241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10161183	0.97[ASN][1000 genomes]
rs10444553	0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876208	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169258	1.00[ASW][hapmap]
rs11169482	1.00[ASW][hapmap];0.90[JPT][hapmap]
rs11169518	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11169519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11169535	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11169616	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11169760	0.95[ASN][1000 genomes]
rs11169768	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169807	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs1400285	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1403521	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1516558	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1523118	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523121	0.95[ASN][1000 genomes]
rs1586373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2138543	0.82[AMR][1000 genomes]
rs2388172	0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34246358	0.92[ASN][1000 genomes]
rs35749392	0.96[ASN][1000 genomes]
rs3759139	1.00[ASW][hapmap]
rs3803020	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4384412	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4595586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616077	1.00[ASW][hapmap]
rs4768388	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56149694	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56344858	0.94[ASN][1000 genomes]
rs6580849	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7314227	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315271	1.00[ASW][hapmap];0.90[JPT][hapmap]
rs7957376	0.90[JPT][hapmap]
rs7957999	0.85[ASN][1000 genomes]
rs7962363	0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7970097	0.92[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs7980448	0.81[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	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1400280	SYT10	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39203200-39276000	Weak transcription	Aorta	Aorta
2	chr12:39204000-39284800	Weak transcription	Lung	lung
3	chr12:39206600-39243800	Weak transcription	Left Ventricle	heart
4	chr12:39206600-39249200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:39206800-39241400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:39206800-39241400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:39219200-39242600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:39221800-39251800	Weak transcription	Liver	Liver
9	chr12:39224000-39241800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:39229400-39252200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:39232400-39247600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:39233200-39241800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:39233200-39244000	Weak transcription	Right Atrium	heart
14	chr12:39233200-39245800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:39238800-39271600	Weak transcription	NHEK	skin
16	chr12:39239200-39242400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:39239200-39284000	Weak transcription	Hela-S3	cervix
18	chr12:39240400-39244000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:39240800-39242000	Strong transcription	GM12878-XiMat	blood
20	chr12:39240800-39242000	Enhancers	HUVEC	blood vessel
21	chr12:39241000-39241400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:39241000-39241400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:39241200-39241400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr12:39241200-39241800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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