Variant report

Variant	rs299477
Chromosome Location	chr12:29706904-29706905
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29692484..29694062-chr12:29704393..29706971,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11829731	0.91[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap]
rs11829994	0.83[CEU][hapmap]
rs11834291	0.91[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap]
rs12310251	0.83[CEU][hapmap]
rs12424239	0.80[CEU][hapmap]
rs12822100	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12826893	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12826911	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12828728	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs142565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs148897	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs159684	0.91[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs159688	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs159691	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs159692	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs16934418	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs16934448	1.00[CEU][hapmap]
rs16934474	0.95[TSI][hapmap]
rs16934523	0.89[CHB][hapmap]
rs16934537	0.89[CHB][hapmap]
rs16934564	0.89[CHB][hapmap]
rs16934569	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs16934597	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs16934635	1.00[CHB][hapmap]
rs2288228	0.95[TSI][hapmap]
rs299478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs299480	0.81[AFR][1000 genomes]
rs299482	0.89[CHB][hapmap]
rs299483	0.89[CHB][hapmap]
rs299484	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs299485	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs34384320	1.00[ASN][1000 genomes]
rs7301943	0.91[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[TSI][hapmap]
rs7315541	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs299477	SYT10	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:29673600-29708800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:29691200-29709200	Weak transcription	HMEC	breast
5	chr12:29698200-29712600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:29699400-29709600	Weak transcription	Left Ventricle	heart
7	chr12:29699400-29715800	Weak transcription	Right Ventricle	heart
8	chr12:29699800-29708800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:29700000-29712000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:29700200-29712200	Weak transcription	Ovary	ovary
11	chr12:29700400-29712000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
14	chr12:29700600-29708800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:29700600-29711400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:29700800-29707400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:29700800-29709000	Weak transcription	HSMM	muscle
18	chr12:29700800-29709600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:29701000-29709400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:29701000-29714200	Weak transcription	HSMMtube	muscle
21	chr12:29701200-29714400	Weak transcription	NHDF-Ad	bronchial
22	chr12:29701200-29714400	Weak transcription	NHLF	lung
23	chr12:29701200-29715200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:29701200-29715600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:29701400-29711600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:29703800-29715200	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:29704000-29709200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:29705000-29711600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:29705000-29716000	Weak transcription	Spleen	Spleen
30	chr12:29705600-29707200	Enhancers	Hela-S3	cervix
31	chr12:29705800-29707400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr12:29706000-29715200	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:29706200-29707000	Weak transcription	Fetal Kidney	kidney
34	chr12:29706200-29708800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:29706200-29715000	Weak transcription	Osteobl	bone
36	chr12:29706400-29708800	Weak transcription	Adipose Nuclei	Adipose
37	chr12:29706400-29709000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:29706400-29711600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:29706600-29708800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:29706600-29709400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:29706600-29716200	Weak transcription	Aorta	Aorta
42	chr12:29706800-29707400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:29706800-29711400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:29706800-29712200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:29706800-29712200	Weak transcription	Liver	Liver

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