Variant report

Variant	rs7149412
Chromosome Location	chr14:104384035-104384036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:104384009-104384516	HepG2	liver:	n/a	n/a
2	POLR2A	chr14:104383934-104384130	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr14:104383857-104384653	K562	blood:	n/a	n/a
4	POLR2A	chr14:104383825-104384665	K562	blood:	n/a	n/a
5	POLR2A	chr14:104383997-104384159	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:104383999..104386148-chr14:104386377..104388170,2	MCF-7	breast:
2	chr14:104380212..104384984-chr14:104386073..104389493,7	MCF-7	breast:
3	chr14:104382782..104384998-chr14:104387935..104389559,2	K562	blood:
4	chr14:104380356..104382278-chr14:104382804..104385092,2	MCF-7	breast:
5	chr14:104383824..104385771-chr14:104411318..104413343,2	K562	blood:
6	chr14:104377058..104380322-chr14:104382660..104385611,3	MCF-7	breast:
7	chr14:104383824..104386788-chr14:104411318..104413343,3	K562	blood:

No data

Variant related genes	Relation type
C14orf2	TF binding region
ENSG00000156411	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10139271	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10139483	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10149351	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10149630	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10467890	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11160773	0.85[CEU][hapmap];0.87[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11160778	0.81[CHB][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs11160783	0.81[TSI][hapmap]
rs11160784	0.81[CHB][hapmap];0.86[TSI][hapmap]
rs11623042	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11625083	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11626960	0.81[CHB][hapmap]
rs11628540	0.81[CHB][hapmap]
rs11628717	0.81[CHB][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs12886010	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12890969	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12895187	0.81[CHB][hapmap]
rs12896676	0.81[CHB][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs1770998	0.81[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2208431	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2273842	0.81[CHB][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs28505294	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28592598	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2887389	0.81[AMR][1000 genomes]
rs4900607	0.87[CHB][hapmap];0.90[TSI][hapmap]
rs4906389	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4906391	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4906395	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7143739	0.81[CHB][hapmap]
rs7147107	0.85[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7150461	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7154082	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7156122	0.81[CHB][hapmap]
rs7160557	0.81[CHB][hapmap]
rs7161468	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8003075	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9324066	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9671921	0.80[CEU][hapmap];0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	nsv1048353	chr14:104361402-104483286	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases
10	nsv902322	chr14:104365310-104464809	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv902323	chr14:104381687-104464809	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7149412	TDRD9	cis	cerebellum	SCAN
rs7149412	C14orf2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104363200-104387000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:104375000-104385800	Weak transcription	Small Intestine	intestine
3	chr14:104375800-104384200	Strong transcription	Dnd41	blood
4	chr14:104376000-104384800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr14:104376600-104384200	Weak transcription	Right Atrium	heart
6	chr14:104376800-104386200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:104376800-104387000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr14:104376800-104387000	Weak transcription	Stomach Mucosa	stomach
9	chr14:104377200-104384800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr14:104377200-104385600	Strong transcription	Fetal Intestine Small	intestine
11	chr14:104377200-104386400	Weak transcription	Fetal Heart	heart
12	chr14:104377200-104386800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr14:104377400-104384400	Strong transcription	Placenta	Placenta
14	chr14:104377400-104384600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:104377400-104384600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr14:104377400-104384600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr14:104377400-104384600	Strong transcription	Liver	Liver
18	chr14:104377400-104384600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr14:104377400-104384600	Strong transcription	Fetal Intestine Large	intestine
20	chr14:104377400-104384600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr14:104377400-104384600	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr14:104377400-104384800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr14:104377400-104384800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr14:104377400-104384800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr14:104377400-104384800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr14:104377400-104384800	Strong transcription	Thymus	Thymus
27	chr14:104377400-104385200	Strong transcription	Fetal Brain Female	brain
28	chr14:104377400-104385200	Strong transcription	Fetal Muscle Leg	muscle
29	chr14:104377400-104386000	Strong transcription	Fetal Stomach	stomach
30	chr14:104377600-104384200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr14:104377600-104384400	Strong transcription	Spleen	Spleen
32	chr14:104377600-104384600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr14:104377600-104384600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr14:104377600-104384600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr14:104377600-104384600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr14:104377600-104384600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr14:104377600-104384600	Strong transcription	A549	lung
38	chr14:104377600-104384800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr14:104377600-104384800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr14:104377600-104384800	Strong transcription	Fetal Thymus	thymus
41	chr14:104377600-104385200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:104377800-104384600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr14:104377800-104384600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr14:104377800-104384600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr14:104377800-104384600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr14:104377800-104384600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr14:104377800-104384600	Strong transcription	Brain Anterior Caudate	brain
48	chr14:104377800-104384800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:104377800-104384800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr14:104378000-104385200	Strong transcription	Lung	lung

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