Variant report

Variant	rs11624462
Chromosome Location	chr14:35671686-35671687
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:35670539..35672448-chr14:35874285..35876170,2	MCF-7	breast:
2	chr14:35665653..35668346-chr14:35670168..35673640,4	K562	blood:
3	chr14:35665653..35667827-chr14:35670189..35673146,2	K562	blood:
4	chr14:35670106..35671869-chr14:35871133..35873972,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPP2R3C-4	chr14:35668509-35676125	l_962_chr14:35668508-35676460_thyroid

Variant related genes	Relation type
ENSG00000100906	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10444669	0.84[ASN][1000 genomes]
rs10483452	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11156878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11620737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11620951	0.90[ASN][1000 genomes]
rs11623882	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11625046	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs11625810	0.84[ASN][1000 genomes]
rs11625942	0.84[ASN][1000 genomes]
rs11626113	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs11627092	0.80[AFR][1000 genomes]
rs11627958	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11628446	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12881415	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs12888766	1.00[YRI][hapmap]
rs1475041	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1712354	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs17458312	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1963154	0.80[AFR][1000 genomes]
rs2057337	1.00[JPT][hapmap]
rs34319196	0.86[ASN][1000 genomes]
rs34658054	0.86[ASN][1000 genomes]
rs34844770	0.86[ASN][1000 genomes]
rs35361707	0.86[ASN][1000 genomes]
rs35468265	0.84[ASN][1000 genomes]
rs35861323	0.86[ASN][1000 genomes]
rs4432181	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4982263	0.88[YRI][hapmap]
rs55693281	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55805245	0.84[ASN][1000 genomes]
rs55815172	0.84[ASN][1000 genomes]
rs56240056	0.84[ASN][1000 genomes]
rs56380926	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988266	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988267	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs61988269	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs61988270	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs61988271	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs61988276	0.90[AFR][1000 genomes]
rs61989495	0.84[ASN][1000 genomes]
rs61989543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61989544	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989545	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61989546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61989547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66539779	0.86[ASN][1000 genomes]
rs7153434	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7155760	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7158151	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7158706	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs799456	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs799467	0.88[YRI][hapmap]
rs799493	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs8013647	0.88[YRI][hapmap]
rs8018597	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8018657	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs8021880	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking 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	73 gene(s)	inside rSNPs	diseases
2	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	65 gene(s)	inside rSNPs	diseases
4	nsv564264	chr14:35482797-35732369	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1044515	chr14:35510785-35756317	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv1046992	chr14:35527239-35724227	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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	27 gene(s)	inside rSNPs	diseases
8	nsv1051274	chr14:35529529-35724227	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv1048823	chr14:35537281-35724892	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
10	nsv542032	chr14:35537281-35724892	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv1040540	chr14:35537481-35724753	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv542033	chr14:35537481-35724753	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1042625	chr14:35546094-35680358	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
14	nsv1050123	chr14:35546114-35724892	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
15	nsv542034	chr14:35546114-35724892	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv1043692	chr14:35548276-35720016	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
18	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
19	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11624462	PPP2R3C	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35628600-35672000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:35643400-35671800	Weak transcription	Fetal Thymus	thymus
3	chr14:35643400-35724000	Weak transcription	Left Ventricle	heart
4	chr14:35650400-35682200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:35650600-35702600	Weak transcription	Liver	Liver
6	chr14:35650800-35707800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr14:35655800-35691800	Weak transcription	Psoas Muscle	Psoas
8	chr14:35660400-35683200	Weak transcription	HSMMtube	muscle
9	chr14:35661000-35672200	Weak transcription	Aorta	Aorta
10	chr14:35661000-35683400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:35661000-35690000	Weak transcription	Fetal Stomach	stomach
12	chr14:35661000-35736400	Weak transcription	Fetal Intestine Small	intestine
13	chr14:35661400-35682200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr14:35661600-35683000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr14:35663200-35680200	Weak transcription	Primary B cells from cord blood	blood
16	chr14:35666200-35671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr14:35666200-35681800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr14:35666200-35683600	Weak transcription	GM12878-XiMat	blood
19	chr14:35666400-35682200	Weak transcription	HSMM	muscle
20	chr14:35666400-35682400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr14:35666400-35682400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr14:35666400-35683000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr14:35667400-35673200	Weak transcription	A549	lung
24	chr14:35667400-35681400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr14:35667800-35682000	Weak transcription	NHEK	skin
26	chr14:35667800-35682800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr14:35670000-35675600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr14:35670200-35672200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr14:35670200-35672400	Enhancers	Primary T cells from cord blood	blood
30	chr14:35670200-35672400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr14:35670200-35673200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr14:35670200-35675600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr14:35670200-35675600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr14:35670400-35673200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr14:35670800-35673200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr14:35670800-35676000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:35670800-35691800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr14:35671200-35672000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr14:35671200-35672400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr14:35671200-35675600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr14:35671200-35675600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr14:35671400-35673600	Enhancers	Primary hematopoietic stem cells	blood
43	chr14:35671400-35674000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr14:35671400-35674400	Enhancers	Dnd41	blood
45	chr14:35671400-35675600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr14:35671600-35672200	Enhancers	Thymus	Thymus
47	chr14:35671600-35672200	Enhancers	HepG2	liver
48	chr14:35671600-35672800	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr14:35671600-35673200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr14:35671600-35674400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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