Variant report

Variant	rs12718061
Chromosome Location	chr3:196347437-196347438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196345698..196350992-chr3:196355970..196361124,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232065	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12718062	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1385331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34088166	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34515026	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3964454	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6583331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6799977	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807839	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7614184	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9824819	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]

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	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12718061	LRRC33	cis	multi-tissue	Pritchard
rs12718061	NCBP2	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196339600-196354800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:196339800-196351000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:196340600-196350200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:196343000-196349200	Enhancers	Primary hematopoietic stem cells	blood
5	chr3:196343400-196351000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:196344200-196347600	Enhancers	Fetal Intestine Small	intestine
7	chr3:196344600-196350200	Weak transcription	Primary T cells from cord blood	blood
8	chr3:196344600-196351000	Weak transcription	Thymus	Thymus
9	chr3:196345400-196351200	Enhancers	Fetal Thymus	thymus
10	chr3:196345600-196347600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:196345600-196347600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:196345600-196347800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:196345800-196347600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:196345800-196347600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:196345800-196347800	Enhancers	Rectal Smooth Muscle	rectum
16	chr3:196346000-196347600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:196346000-196347600	Enhancers	K562	blood
18	chr3:196346000-196347800	Enhancers	HUVEC	blood vessel
19	chr3:196346000-196348600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:196346200-196347600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:196346200-196347600	Enhancers	Brain Hippocampus Middle	brain
22	chr3:196346200-196349200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:196346200-196350000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:196346400-196351200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:196346400-196351200	Weak transcription	Dnd41	blood
26	chr3:196346800-196347600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr3:196346800-196347600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:196346800-196347600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:196346800-196351000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:196347000-196347600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:196347000-196347600	Enhancers	Primary B cells from peripheral blood	blood
32	chr3:196347000-196347600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:196347000-196347600	Enhancers	Adipose Nuclei	Adipose
34	chr3:196347000-196347600	Enhancers	Duodenum Mucosa	Duodenum
35	chr3:196347000-196347800	Enhancers	Stomach Smooth Muscle	stomach
36	chr3:196347000-196347800	Flanking Active TSS	GM12878-XiMat	blood
37	chr3:196347000-196348000	Enhancers	Primary B cells from cord blood	blood
38	chr3:196347000-196348400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr3:196347200-196347600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr3:196347200-196347600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:196347200-196347600	Enhancers	Fetal Heart	heart
42	chr3:196347200-196347800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr3:196347200-196348200	Enhancers	Spleen	Spleen
44	chr3:196347200-196350200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:196347200-196350200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:196347200-196350200	Weak transcription	Brain Angular Gyrus	brain
47	chr3:196347200-196350200	Weak transcription	Brain Substantia Nigra	brain
48	chr3:196347200-196351200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:196347200-196351400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:196347200-196354200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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