Variant report

Variant	rs17103104
Chromosome Location	chr14:35690978-35690979
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:35689608..35693753-chr14:35865249..35869361,6	MCF-7	breast:
2	chr14:35689499..35691872-chr14:35695330..35698376,3	MCF-7	breast:
3	chr14:35688330..35694959-chr14:35872168..35876310,11	MCF-7	breast:
4	chr14:35688349..35704994-chr14:35861790..35878218,62	MCF-7	breast:
5	chr14:35689551..35692151-chr14:35760450..35762726,3	MCF-7	breast:
6	chr14:35686289..35689238-chr14:35690846..35692653,2	K562	blood:
7	chr14:35687707..35690246-chr14:35690578..35692404,2	MCF-7	breast:
8	chr14:35688941..35691439-chr14:35716657..35719579,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPP2R3C-4	chr14:35690827-35691028	l_962_chr14:35668508-35676460_thyroid

No data

Variant related genes	Relation type
ENSG00000100906	Chromatin interaction
ENSG00000100902	Chromatin interaction
ENSG00000265530	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1028449	0.92[CEU][hapmap]
rs1048990	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11156875	0.92[CEU][hapmap];0.96[TSI][hapmap]
rs12586305	0.92[EUR][1000 genomes]
rs17091835	1.00[MEX][hapmap]
rs17103120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17103226	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.92[AFR][1000 genomes]
rs17113838	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2143950	0.92[CEU][hapmap]
rs3809449	0.85[CEU][hapmap];0.96[TSI][hapmap]
rs4272943	0.82[ASW][hapmap];0.81[MEX][hapmap]
rs4594164	0.92[CEU][hapmap];1.00[TSI][hapmap]
rs57275892	0.88[EUR][1000 genomes]
rs7144423	1.00[CEU][hapmap]
rs7144617	0.92[TSI][hapmap]
rs7145474	0.85[CEU][hapmap]
rs7153550	0.92[TSI][hapmap]
rs7156322	0.92[CEU][hapmap]
rs7159324	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs8014377	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs941653	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
14	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
15	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
16	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
17	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
18	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
19	nsv564314	chr14:35684196-35702857	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv564315	chr14:35684196-35703839	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	esv2754534	chr14:35690978-35744839	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17103104	PPP2R3C	cis	Whole Blood	GTEx
rs17103104	KIAA0391	Cis_1M	lymphoblastoid	RTeQTL
rs17103104	KIAA0391	cis	multi-tissue	Pritchard
rs17103104	C14orf10	cis	multi-tissue	Pritchard
rs17103104	PPP2R3C	Cis_1M	lymphoblastoid	RTeQTL
rs17103104	NKX2-1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35643400-35724000	Weak transcription	Left Ventricle	heart
2	chr14:35650600-35702600	Weak transcription	Liver	Liver
3	chr14:35650800-35707800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr14:35655800-35691800	Weak transcription	Psoas Muscle	Psoas
5	chr14:35661000-35736400	Weak transcription	Fetal Intestine Small	intestine
6	chr14:35670800-35691800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr14:35672000-35742200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr14:35672200-35700000	Weak transcription	Thymus	Thymus
9	chr14:35673600-35691200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr14:35674400-35698600	Weak transcription	Dnd41	blood
11	chr14:35674400-35699600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr14:35674400-35711200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr14:35674800-35737000	Weak transcription	Lung	lung
14	chr14:35675600-35691400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr14:35675600-35692200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr14:35675600-35699200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr14:35678000-35719600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr14:35679600-35699400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr14:35679800-35692000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr14:35679800-35699800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr14:35680000-35698600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr14:35680200-35691600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr14:35680400-35691800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr14:35680800-35729800	Weak transcription	Primary B cells from cord blood	blood
25	chr14:35681000-35729800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr14:35683600-35691600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr14:35683600-35693600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr14:35683800-35693200	Weak transcription	NH-A	brain
29	chr14:35683800-35693200	Weak transcription	NHLF	lung
30	chr14:35684000-35706800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:35684600-35691000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:35684600-35699000	Weak transcription	GM12878-XiMat	blood
33	chr14:35684600-35737000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr14:35684600-35760800	Weak transcription	HSMM	muscle
35	chr14:35684800-35693000	Weak transcription	HSMMtube	muscle
36	chr14:35684800-35703000	Weak transcription	HMEC	breast
37	chr14:35685000-35693200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr14:35685000-35699800	Weak transcription	Fetal Lung	lung
39	chr14:35685200-35698800	Weak transcription	Hela-S3	cervix
40	chr14:35686800-35693600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr14:35686800-35735800	Weak transcription	Fetal Intestine Large	intestine
42	chr14:35687000-35692000	Strong transcription	HepG2	liver
43	chr14:35687400-35716400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr14:35688000-35691600	Strong transcription	Primary T cells from cord blood	blood
45	chr14:35688600-35691800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr14:35688600-35699000	Weak transcription	Fetal Thymus	thymus
47	chr14:35688800-35699400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr14:35689000-35699000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr14:35689600-35691000	Enhancers	NHDF-Ad	bronchial
50	chr14:35689600-35692000	Weak transcription	Monocytes-CD14+_RO01746	blood

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