Variant report

Variant	rs1252290
Chromosome Location	chr12:67412186-67412187
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1109345	0.98[EUR][1000 genomes]
rs1252288	0.88[ASN][1000 genomes]
rs1252289	0.98[EUR][1000 genomes]
rs1252291	0.88[ASN][1000 genomes]
rs12580718	1.00[ASN][1000 genomes]
rs1270488	0.88[ASN][1000 genomes]
rs710631	0.88[ASN][1000 genomes]
rs774386	0.88[ASN][1000 genomes]
rs774388	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs774395	0.90[ASN][1000 genomes]
rs774397	0.98[EUR][1000 genomes]
rs774398	0.97[EUR][1000 genomes]
rs774399	0.88[ASN][1000 genomes]
rs774400	0.88[ASN][1000 genomes]
rs905693	0.98[EUR][1000 genomes]
rs941095	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036984	chr12:67273098-67427543	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1041160	chr12:67357870-67439696	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv469462	chr12:67361657-67475906	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv559211	chr12:67361657-67475906	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1053249	chr12:67395538-67417828	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1046591	chr12:67396219-67423067	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2762986	chr12:67409191-67413365	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1252290	FAM19A2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67397000-67412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:67408600-67412200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:67409600-67412400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:67409600-67412400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:67409800-67412200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:67409800-67412200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:67409800-67412400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:67409800-67412400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:67409800-67412800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:67409800-67420800	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:67409800-67420800	Weak transcription	Right Atrium	heart
12	chr12:67410200-67412600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:67410200-67412600	Weak transcription	Fetal Brain Male	brain
14	chr12:67410800-67412600	Weak transcription	Brain Germinal Matrix	brain
15	chr12:67411400-67412800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr12:67411600-67413200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr12:67411600-67413400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr12:67411800-67413200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:67411800-67413200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr12:67411800-67413400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr12:67411800-67413400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr12:67412000-67412200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:67412000-67412400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:67412000-67412400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:67412000-67412800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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