Variant report

Variant	rs879448
Chromosome Location	chr14:105393707-105393708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr14:105393620-105393770	GM12865	blood:	n/a	chr14:105393737-105393746
2	CTCF	chr14:105393700-105393850	GM12870	blood:	n/a	chr14:105393737-105393746
3	CTCF	chr14:105393640-105393790	HCPEpiC	choroid plexus:	n/a	chr14:105393737-105393746
4	CTCF	chr14:105393560-105393710	HEK293	kidney:	n/a	n/a
5	CTCF	chr14:105393700-105393850	HUVEC	blood vessel:	n/a	chr14:105393737-105393746
6	CTCF	chr14:105393653-105393857	H1-hESC	embryonic stem cell:	n/a	chr14:105393737-105393746
7	CTCF	chr14:105393600-105393750	WERI-Rb-1	eye:	n/a	chr14:105393737-105393746
8	CTCF	chr14:105393640-105393790	GM12871	blood:	n/a	chr14:105393737-105393746
9	CTCF	chr14:105393560-105393710	GM12866	blood:	n/a	n/a
10	CTCF	chr14:105393700-105393850	GM12868	blood:	n/a	chr14:105393737-105393746
11	CTCF	chr14:105393620-105393770	GM12866	blood:	n/a	chr14:105393737-105393746
12	CTCF	chr14:105393580-105393730	AG09309	skin:	n/a	n/a
13	CTCF	chr14:105393620-105393770	HVMF	connective:	n/a	chr14:105393737-105393746
14	CTCF	chr14:105393700-105393850	HBMEC	blood vessel:	n/a	chr14:105393737-105393746
15	CTCF	chr14:105393660-105393810	GM12874	blood:	n/a	chr14:105393737-105393746
16	CTCF	chr14:105393680-105393830	HUVEC	blood vessel:	n/a	chr14:105393737-105393746
17	CTCF	chr14:105393680-105393830	GM12865	blood:	n/a	chr14:105393737-105393746
18	CTCF	chr14:105393600-105393750	GM12870	blood:	n/a	chr14:105393737-105393746
19	CTCF	chr14:105393680-105393830	GM12869	blood:	n/a	chr14:105393737-105393746
20	CTCF	chr14:105393640-105393790	GM12864	blood:	n/a	chr14:105393737-105393746
21	CTCF	chr14:105393640-105393790	GM12872	blood:	n/a	chr14:105393737-105393746
22	ZBTB7A	chr14:105393685-105393905	K562	blood:	n/a	n/a
23	ZBTB7A	chr14:105393633-105393914	K562	blood:	n/a	n/a
24	CTCF	chr14:105393600-105393750	GM12875	blood:	n/a	chr14:105393737-105393746
25	CTCF	chr14:105393541-105393835	H1-hESC	embryonic stem cell:	n/a	chr14:105393737-105393746
26	CTCF	chr14:105393680-105393830	WI-38	lung:	n/a	chr14:105393737-105393746
27	CTCF	chr14:105393600-105393750	GM12869	blood:	n/a	chr14:105393737-105393746
28	CTCF	chr14:105393620-105393770	HepG2	liver:	n/a	chr14:105393737-105393746
29	CTCF	chr14:105393560-105393710	HAc	cerebellar:	n/a	n/a
30	CTCF	chr14:105393660-105393810	GM12873	blood:	n/a	chr14:105393737-105393746
31	CTCF	chr14:105393700-105393850	GM12873	blood:	n/a	chr14:105393737-105393746
32	CTCF	chr14:105393640-105393790	AG04449	skin:	n/a	chr14:105393737-105393746
33	CTCF	chr14:105393600-105393750	GM12867	blood:	n/a	chr14:105393737-105393746
34	CTCF	chr14:105393600-105393750	GM12872	blood:	n/a	chr14:105393737-105393746
35	CTCF	chr14:105393660-105393810	GM12864	blood:	n/a	chr14:105393737-105393746

No.	Distal block	Cell Line	Cell type
1	chr14:105387983..105391489-chr14:105392006..105395629,4	MCF-7	breast:
2	chr14:105391507..105394096-chr14:105419228..105421927,2	MCF-7	breast:
3	chr14:105393329..105396153-chr14:105398779..105401055,3	MCF-7	breast:
4	chr14:105391640..105393998-chr14:105436679..105438519,2	MCF-7	breast:
5	chr14:105392936..105394714-chr14:105435765..105438591,2	MCF-7	breast:

Variant related genes	Relation type
PLD4	TF binding region
ENSG00000166428	Chromatin interaction
ENSG00000185567	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10083490	0.80[EUR][1000 genomes]
rs10083496	0.80[EUR][1000 genomes]
rs10137166	1.00[JPT][hapmap]
rs10141053	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10145566	0.80[EUR][1000 genomes]
rs10149193	0.80[EUR][1000 genomes]
rs10152073	0.80[EUR][1000 genomes]
rs1036713	0.84[EUR][1000 genomes]
rs10438246	0.80[EUR][1000 genomes]
rs1048257	0.80[EUR][1000 genomes]
rs11160825	0.80[EUR][1000 genomes]
rs11160827	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11623422	0.80[EUR][1000 genomes]
rs11848564	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11851053	0.80[EUR][1000 genomes]
rs12885004	0.83[EUR][1000 genomes]
rs2582529	0.93[EUR][1000 genomes]
rs2582531	0.92[CEU][hapmap];0.97[EUR][1000 genomes]
rs2582533	0.83[EUR][1000 genomes]
rs2819422	0.80[EUR][1000 genomes]
rs2819424	0.80[EUR][1000 genomes]
rs2819439	0.93[EUR][1000 genomes]
rs2819468	0.96[EUR][1000 genomes]
rs2819469	0.86[EUR][1000 genomes]
rs28380382	0.80[EUR][1000 genomes]
rs2841268	0.93[EUR][1000 genomes]
rs2841269	0.84[EUR][1000 genomes]
rs2841276	0.84[EUR][1000 genomes]
rs2841277	0.83[EUR][1000 genomes]
rs2841278	0.86[EUR][1000 genomes]
rs2841280	0.87[EUR][1000 genomes]
rs2841281	0.86[EUR][1000 genomes]
rs28454709	0.80[EUR][1000 genomes]
rs28600075	0.80[EUR][1000 genomes]
rs2919624	0.92[EUR][1000 genomes]
rs3001424	0.92[EUR][1000 genomes]
rs34499888	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3742935	0.80[EUR][1000 genomes]
rs4465542	0.80[EUR][1000 genomes]
rs61421370	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8004038	0.82[EUR][1000 genomes]
rs874753	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672139	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053591	chr14:105024558-105475931	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv542224	chr14:105024558-105475931	Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1828345	chr14:105100787-105803170	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
4	nsv542225	chr14:105133688-105803170	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
5	nsv542227	chr14:105157572-105803170	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
6	nsv456456	chr14:105285159-105412541	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv566099	chr14:105285159-105412541	Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv917106	chr14:105339195-105803170	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv566139	chr14:105347296-105417147	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv902419	chr14:105381763-105494262	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1049253	chr14:105384959-105471855	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv542228	chr14:105390569-105459912	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs879448	TDRD9	cis	Thyroid	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105390800-105394000	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr14:105391000-105394000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr14:105391000-105395400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:105391200-105394200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr14:105391600-105394200	Enhancers	Fetal Thymus	thymus
6	chr14:105391600-105395000	Enhancers	Fetal Intestine Small	intestine
7	chr14:105391600-105398600	Weak transcription	Gastric	stomach
8	chr14:105391800-105394200	Enhancers	Spleen	Spleen
9	chr14:105392200-105394200	Enhancers	Fetal Muscle Leg	muscle
10	chr14:105392200-105395800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr14:105392600-105393800	Weak transcription	Fetal Intestine Large	intestine
12	chr14:105392600-105394400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr14:105392600-105394600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:105392800-105393800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr14:105392800-105393800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr14:105393000-105394200	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr14:105393200-105394000	Enhancers	Esophagus	oesophagus
18	chr14:105393200-105394200	Enhancers	Primary hematopoietic stem cells	blood
19	chr14:105393400-105394400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr14:105393600-105393800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
21	chr14:105393600-105393800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr14:105393600-105393800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
23	chr14:105393600-105394000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr14:105393600-105394200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr14:105393600-105394200	Bivalent Enhancer	Adipose Nuclei	Adipose
26	chr14:105393600-105394200	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr14:105393600-105394400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr14:105393600-105394400	Enhancers	GM12878-XiMat	blood
29	chr14:105393600-105394600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr14:105393600-105396000	Bivalent Enhancer	Placenta	Placenta

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