Variant report

Variant	rs17702574
Chromosome Location	chr12:4940228-4940229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10849145	1.00[JPT][hapmap]
rs10849152	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849153	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366826	1.00[JPT][hapmap]
rs12815178	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489576	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7953164	0.85[AMR][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	nsv520570	chr12:4929787-4954591	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1047238	chr12:4929787-4955435	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17702574	LRTM2	cis	cerebellum	SCAN
rs17702574	CACNB4	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4929200-4966600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:4929400-4966600	Weak transcription	Brain Angular Gyrus	brain
3	chr12:4930800-4942400	Weak transcription	Fetal Brain Male	brain
4	chr12:4934000-4942400	Weak transcription	HSMM	muscle
5	chr12:4935800-4965000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:4937400-4940400	Flanking Active TSS	Dnd41	blood
7	chr12:4938400-4940600	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr12:4938600-4940800	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:4938600-4960200	Weak transcription	Fetal Brain Female	brain
10	chr12:4939000-4941800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:4939200-4940400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:4939200-4940800	Enhancers	Fetal Thymus	thymus
13	chr12:4939200-4943000	Enhancers	Primary B cells from peripheral blood	blood
14	chr12:4939200-4959400	Weak transcription	Brain Germinal Matrix	brain
15	chr12:4939400-4940400	Enhancers	Primary T cells from cord blood	blood
16	chr12:4939400-4940400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr12:4939400-4940400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:4939400-4940400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr12:4939400-4940400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:4939400-4940800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:4939600-4940400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:4939600-4941400	Enhancers	Primary B cells from cord blood	blood
23	chr12:4939600-4942400	Weak transcription	HSMMtube	muscle
24	chr12:4939600-4966600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:4939800-4940800	Enhancers	Fetal Stomach	stomach
26	chr12:4939800-4941000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:4940200-4940400	Bivalent Enhancer	Fetal Intestine Small	intestine
28	chr12:4940200-4941400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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