Variant report

Variant	rs12714948
Chromosome Location	chr3:17604963-17604964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10510476	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[MKK][hapmap]
rs10510479	1.00[CEU][hapmap]
rs17043520	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[MKK][hapmap]
rs17043521	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[MKK][hapmap]
rs17043523	1.00[CEU][hapmap]
rs17043525	1.00[CEU][hapmap]
rs17043527	1.00[CEU][hapmap]
rs17043529	1.00[CEU][hapmap]
rs17043556	1.00[CEU][hapmap]
rs17043562	1.00[CEU][hapmap]
rs17043615	1.00[CEU][hapmap]
rs17043634	1.00[CEU][hapmap]
rs17043847	1.00[CEU][hapmap]
rs17043853	1.00[CEU][hapmap]
rs17043870	1.00[CEU][hapmap]
rs17043872	1.00[CEU][hapmap]
rs17043877	1.00[CEU][hapmap]
rs17043895	1.00[CEU][hapmap]
rs4331697	1.00[CEU][hapmap]
rs4579004	1.00[CEU][hapmap]
rs6795454	1.00[CEU][hapmap]
rs6804323	1.00[CEU][hapmap]
rs9754654	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876590	chr3:17230884-17604963	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv876591	chr3:17246392-17671992	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv915606	chr3:17357042-17668263	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999460	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv536510	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv876592	chr3:17369313-17604963	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv876593	chr3:17419843-17604963	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1013069	chr3:17560456-17783372	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12714948	PLCL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17575000-17607600	Weak transcription	Dnd41	blood
2	chr3:17575000-17613400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:17580000-17619400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:17581200-17606200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr3:17584000-17613200	Weak transcription	GM12878-XiMat	blood
6	chr3:17584200-17608600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:17587000-17613600	Weak transcription	Primary B cells from cord blood	blood
8	chr3:17596000-17619600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:17600400-17610400	Weak transcription	A549	lung
10	chr3:17603600-17607400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:17604600-17605000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:17604800-17605000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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