Variant report

Variant	rs6576012
Chromosome Location	chr14:104400159-104400160
allele	C/T
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:104399690..104401761-chr14:104403081..104405618,2	K562	blood:
2	chr14:104385987..104387958-chr14:104398361..104401155,2	MCF-7	breast:
3	chr14:104394897..104396539-chr14:104399297..104402064,2	MCF-7	breast:
4	chr14:104400120..104402233-chr14:104410455..104413050,2	MCF-7	breast:
5	chr14:104399167..104401671-chr14:104406191..104408805,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C14orf2-1	chr14:104398863-104400802	l_1076_chr14:104398227-104400802_kidney

No data

Variant related genes	Relation type
ENSG00000156414	Chromatin interaction
ENSG00000227729	Chromatin interaction
ENSG00000156411	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10136440	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10149651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11160774	0.90[AMR][1000 genomes]
rs11622475	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11625697	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11626404	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1187446	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1187448	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12885873	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12889168	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12895359	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12895592	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17101911	0.95[CEU][hapmap];0.84[AMR][1000 genomes]
rs1885072	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2005081	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2236246	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2236247	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2269186	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2273610	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2368984	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34288430	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34964872	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56060232	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56231040	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59776579	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7143682	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7143936	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs743212	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8021692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs941946	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	nsv902324	chr14:104399640-104464809	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6576012	TDRD9	cis	Adipose Subcutaneous	GTEx
rs6576012	TDRD9	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104395000-104401200	Weak transcription	Spleen	Spleen
2	chr14:104396600-104400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr14:104397400-104400400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr14:104397800-104400800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:104398400-104400600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr14:104398600-104404600	Weak transcription	Left Ventricle	heart
7	chr14:104399600-104402000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr14:104399800-104400600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:104399800-104400600	Enhancers	HMEC	breast
10	chr14:104400000-104400200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr14:104400000-104400200	Enhancers	HUVEC	blood vessel
12	chr14:104400000-104400400	Enhancers	Primary B cells from cord blood	blood
13	chr14:104400000-104400400	Flanking Active TSS	HepG2	liver
14	chr14:104400000-104400600	Enhancers	Fetal Intestine Large	intestine
15	chr14:104400000-104400600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr14:104400000-104400800	Enhancers	Fetal Intestine Small	intestine
17	chr14:104400000-104400800	Enhancers	NHEK	skin
18	chr14:104400000-104402000	Enhancers	Primary monocytes fromperipheralblood	blood

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