Variant report

Variant	rs13002429
Chromosome Location	chr2:11267366-11267367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11260529..11263397-chr2:11266491..11268422,2	K562	blood:
2	chr2:11256407..11258832-chr2:11266257..11267865,2	MCF-7	breast:
3	chr2:11261636..11264793-chr2:11267057..11269969,4	MCF-7	breast:
4	chr2:11266900..11270015-chr2:11270952..11273853,3	K562	blood:
5	chr2:10971180..10977465-chr2:11267266..11272931,15	MCF-7	breast:
6	chr2:11215555..11217160-chr2:11266403..11268332,2	K562	blood:

Variant related genes	Relation type
ENSG00000143870	Chromatin interaction
ENSG00000145063	Chromatin interaction
ENSG00000150873	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12470798	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12987956	1.00[YRI][hapmap]
rs13021587	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17366322	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2357993	1.00[ASN][1000 genomes]
rs2357994	1.00[ASN][1000 genomes]
rs7608117	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13002429	PQLC3	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11262200-11269800	Weak transcription	Ovary	ovary
2	chr2:11262800-11268600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:11262800-11269600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:11263000-11268400	Weak transcription	HMEC	breast
5	chr2:11263400-11268000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:11263400-11269800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:11263600-11269800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:11263800-11268000	Weak transcription	Spleen	Spleen
9	chr2:11264600-11268600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:11264600-11269600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:11264800-11269800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:11265000-11268400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:11265000-11268400	Weak transcription	Stomach Mucosa	stomach
14	chr2:11265000-11268600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:11265000-11269400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:11265000-11269800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:11265200-11269600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:11265200-11269800	Weak transcription	Liver	Liver
19	chr2:11265400-11268400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:11265400-11269600	Weak transcription	A549	lung
21	chr2:11266600-11268400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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