Variant report

Variant	rs7969141
Chromosome Location	chr12:117214617-117214618
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117214324..117217304-chr12:117220516..117222283,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10744883	0.81[GIH][hapmap]
rs12313074	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1971306	0.83[ASN][1000 genomes]
rs2132389	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4767451	0.94[ASN][1000 genomes]
rs4767453	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6490092	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7297890	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs7299032	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7310216	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs7314211	0.90[MEX][hapmap]
rs7315162	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7961400	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs924079	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1048004	chr12:117170738-117219076	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv1039046	chr12:117170989-117225635	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7969141	C12orf49	cis	parietal	SCAN
rs7969141	MAPKAPK5	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117176800-117217400	Weak transcription	Primary T cells from cord blood	blood
2	chr12:117177000-117217400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:117177000-117224400	Weak transcription	Brain Substantia Nigra	brain
4	chr12:117177200-117216800	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:117177200-117221000	Weak transcription	Fetal Brain Male	brain
6	chr12:117177400-117225800	Weak transcription	HepG2	liver
7	chr12:117177600-117217000	Weak transcription	GM12878-XiMat	blood
8	chr12:117179000-117217200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:117188400-117217000	Weak transcription	Brain Angular Gyrus	brain
10	chr12:117188600-117217000	Weak transcription	Brain Anterior Caudate	brain
11	chr12:117191200-117221000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:117192000-117217000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:117196600-117217000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:117198000-117256200	Weak transcription	Hela-S3	cervix
15	chr12:117198200-117217000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:117198200-117233600	Weak transcription	Fetal Stomach	stomach
17	chr12:117198200-117236600	Weak transcription	A549	lung
18	chr12:117198400-117217000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:117198400-117217600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:117198600-117223800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:117198600-117233600	Weak transcription	Right Atrium	heart
22	chr12:117198800-117220800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:117199600-117215600	Weak transcription	K562	blood
24	chr12:117199600-117217000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:117203200-117217000	Weak transcription	Primary B cells from cord blood	blood
26	chr12:117204800-117216800	Weak transcription	Dnd41	blood
27	chr12:117205200-117216800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr12:117205400-117216200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:117205400-117216800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:117206400-117217000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:117209000-117217000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:117209800-117216800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:117209800-117232600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:117210200-117216800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:117210600-117216600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:117211800-117216600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:117211800-117216800	Weak transcription	Brain Germinal Matrix	brain
38	chr12:117211800-117218000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:117212000-117216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:117212000-117216800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:117212000-117216800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:117212000-117217000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:117212200-117216800	Weak transcription	Fetal Brain Female	brain
44	chr12:117212200-117217000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:117212600-117217000	Weak transcription	Thymus	Thymus
46	chr12:117212800-117214800	Weak transcription	Fetal Thymus	thymus
47	chr12:117213400-117226600	Weak transcription	Fetal Intestine Small	intestine
48	chr12:117213800-117223400	Weak transcription	Placenta	Placenta

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