Variant report

Variant	rs10438243
Chromosome Location	chr14:104345822-104345823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104312778..104315212-chr14:104344720..104347233,3	MCF-7	breast:
2	chr14:104336130..104339253-chr14:104343612..104346035,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTD-2134A5.2.1-2	chr14:104345741-104346670	XLOC_010945
2	lnc-PPP1R13B-1	chr14:104345681-104346641	NONHSAT040223
3	lnc-PPP1R13B-1	chr14:104345681-104346641	NONHSAT040224

Variant related genes	Relation type
ENSG00000258735	Chromatin interaction
ENSG00000088808	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10132641	0.81[ASN][1000 genomes]
rs10133399	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10135198	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10135270	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10139856	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10150898	0.83[EUR][1000 genomes]
rs10438242	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10438244	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12879686	0.89[EUR][1000 genomes]
rs35551424	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35924317	0.89[EUR][1000 genomes]
rs4144027	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4900601	0.92[CEU][hapmap];0.86[CHD][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs55696130	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55924227	0.88[EUR][1000 genomes]
rs56126771	0.89[EUR][1000 genomes]
rs6576010	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71417884	0.87[EUR][1000 genomes]
rs71417885	0.88[EUR][1000 genomes]
rs72712857	0.85[EUR][1000 genomes]
rs761985	0.81[EUR][1000 genomes]
rs8008020	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs8015761	0.82[CEU][hapmap];0.86[CHD][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs881056	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs881057	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs911338	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv902313	chr14:104162263-104378087	Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv902318	chr14:104255083-104464809	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
8	esv1838047	chr14:104283104-104359121	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv902321	chr14:104283104-104378087	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	esv1818596	chr14:104312697-104359121	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1836134	chr14:104312697-104359121	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1053305	chr14:104326137-104372608	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv542205	chr14:104326137-104372608	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv542206	chr14:104326137-104377507	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1042792	chr14:104326137-104384260	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv542207	chr14:104326137-104384260	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv1800828	chr14:104343852-104351500	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10438243	TDRD9	cis	parietal	SCAN
rs10438243	ZFYVE21	cis	cerebellum	SCAN
rs10438243	MARK3	cis	cerebellum	SCAN
rs10438243	C14orf2	cis	cerebellum	SCAN
rs10438243	TDRD9	cis	cerebellum	SCAN
rs10438243	C14orf153	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104339200-104346200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:104339200-104346200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:104339400-104346000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:104339400-104346000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:104339400-104346000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr14:104339400-104346000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr14:104339400-104346000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr14:104339400-104346000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr14:104339400-104346000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr14:104339600-104346000	Weak transcription	Primary T cells from cord blood	blood
11	chr14:104340200-104346000	Weak transcription	Placenta	Placenta
12	chr14:104340200-104346000	Weak transcription	Fetal Stomach	stomach
13	chr14:104340200-104346200	Weak transcription	Fetal Thymus	thymus
14	chr14:104341400-104346400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr14:104341600-104346000	Weak transcription	Lung	lung
16	chr14:104341600-104346000	Weak transcription	Spleen	Spleen
17	chr14:104341600-104346000	Weak transcription	GM12878-XiMat	blood
18	chr14:104341600-104346200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr14:104341600-104346800	Weak transcription	Gastric	stomach
20	chr14:104344000-104346000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr14:104344600-104349800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr14:104345000-104346000	Enhancers	Fetal Lung	lung
23	chr14:104345400-104347400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr14:104345400-104347600	Flanking Active TSS	Liver	Liver
25	chr14:104345600-104346000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr14:104345600-104346200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr14:104345600-104346200	Enhancers	Fetal Intestine Large	intestine
28	chr14:104345600-104346200	Enhancers	Fetal Intestine Small	intestine
29	chr14:104345600-104349800	Enhancers	Fetal Muscle Leg	muscle
30	chr14:104345800-104346000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr14:104345800-104346000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr14:104345800-104346000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr14:104345800-104346000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
34	chr14:104345800-104346000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr14:104345800-104346000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr14:104345800-104346000	Active TSS	Colonic Mucosa	Colon
37	chr14:104345800-104346000	Flanking Active TSS	Stomach Mucosa	stomach
38	chr14:104345800-104346000	Bivalent/Poised TSS	HepG2	liver
39	chr14:104345800-104346000	Enhancers	HMEC	breast
40	chr14:104345800-104346200	Enhancers	Primary B cells from peripheral blood	blood
41	chr14:104345800-104346200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr14:104345800-104346200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
43	chr14:104345800-104346200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr14:104345800-104346200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr14:104345800-104346200	Enhancers	Adipose Nuclei	Adipose
46	chr14:104345800-104346200	Enhancers	Fetal Muscle Trunk	muscle
47	chr14:104345800-104346200	Active TSS	Rectal Smooth Muscle	rectum
48	chr14:104345800-104346200	Enhancers	Right Atrium	heart
49	chr14:104345800-104346400	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr14:104345800-104346400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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