Variant report

Variant	rs6573038
Chromosome Location	chr14:56022792-56022793
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	BHLHE40	chr14:56022774-56022826	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:56022620..56026445-chr14:56044953..56047966,3	MCF-7	breast:
2	chr14:56012207..56014964-chr14:56021875..56024671,2	MCF-7	breast:
3	chr14:56014631..56016749-chr14:56021571..56023338,2	MCF-7	breast:

Variant related genes	Relation type
KTN1	TF binding region
ENSG00000271484	Chromatin interaction
ENSG00000126777	Chromatin interaction
ENSG00000186615	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10148298	0.82[ASN][1000 genomes]
rs12894700	0.91[CEU][hapmap]
rs1951893	0.91[CEU][hapmap]
rs4898867	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4901584	0.91[CEU][hapmap]
rs8006751	0.89[ASN][1000 genomes]
rs8010372	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8011732	0.82[JPT][hapmap]
rs8017185	0.90[CEU][hapmap]
rs942317	0.82[JPT][hapmap];0.91[MEX][hapmap]

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	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1047054	chr14:55922287-56035579	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1037161	chr14:55928030-56039353	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6573038	WDHD1	cis	cerebellum	SCAN
rs6573038	KTN1	cis	multi-tissue	Pritchard
rs6573038	KTN1	cis	parietal	SCAN
rs6573038	CNIH	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56010600-56026600	Weak transcription	Right Ventricle	heart
2	chr14:56010800-56024000	Weak transcription	A549	lung
3	chr14:56014000-56024000	Weak transcription	Pancreas	Pancrea
4	chr14:56014000-56031200	Weak transcription	Left Ventricle	heart
5	chr14:56018600-56023400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:56020800-56023400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:56020800-56023400	Weak transcription	Ovary	ovary
8	chr14:56020800-56023600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:56020800-56024000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:56021000-56023200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr14:56021000-56023400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:56021000-56023400	Weak transcription	HMEC	breast
13	chr14:56021000-56023600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr14:56021000-56023800	Weak transcription	NHEK	skin
15	chr14:56021000-56024000	Weak transcription	Aorta	Aorta
16	chr14:56021000-56026600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr14:56021200-56023600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:56021800-56023600	Enhancers	Fetal Heart	heart
19	chr14:56022000-56023800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr14:56022200-56023000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr14:56022200-56024000	Weak transcription	Psoas Muscle	Psoas
22	chr14:56022600-56026600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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