Variant report

Variant	rs6573042
Chromosome Location	chr14:56031610-56031611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56029954..56032849-chr14:56033323..56035945,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10136386	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs10136408	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs10145555	0.81[EUR][1000 genomes]
rs10146870	0.87[CEU][hapmap]
rs10444721	0.88[CEU][hapmap]
rs12587735	0.88[CEU][hapmap]
rs12882850	0.88[CEU][hapmap]
rs12891489	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs12893162	0.83[CEU][hapmap]
rs12897227	0.88[CEU][hapmap]
rs17684959	0.83[CEU][hapmap]
rs1951887	0.88[CEU][hapmap]
rs2296182	0.88[CEU][hapmap]
rs34872770	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3736877	0.88[CEU][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap];0.84[MKK][hapmap]
rs3765515	0.87[CEU][hapmap]
rs3783654	0.82[CEU][hapmap]
rs4386042	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4457912	0.88[CEU][hapmap]
rs4901585	0.84[AMR][1000 genomes]
rs4901587	0.82[AMR][1000 genomes]
rs4901592	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4901593	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6573053	0.84[CEU][hapmap]
rs6573054	0.88[CEU][hapmap]
rs7158176	0.88[CEU][hapmap]
rs8007832	0.88[CEU][hapmap]
rs8011732	0.84[CEU][hapmap]
rs942317	0.84[CEU][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	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	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
8	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
9	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
10	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
11	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6573042	GCH1	cis	cerebellum	SCAN
rs6573042	KTN1	cis	cerebellum	SCAN
rs6573042	KTN1	cis	parietal	SCAN
rs6573042	FBXO34	cis	parietal	SCAN
rs6573042	KTN1	cis	multi-tissue	Pritchard
rs6573042	CNIH	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56023600-56045200	Weak transcription	Primary T cells from cord blood	blood
2	chr14:56024000-56043200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr14:56024200-56038200	Weak transcription	Brain Hippocampus Middle	brain
4	chr14:56024200-56045400	Weak transcription	Adipose Nuclei	Adipose
5	chr14:56024400-56032400	Weak transcription	Fetal Kidney	kidney
6	chr14:56024400-56035200	Weak transcription	A549	lung
7	chr14:56024400-56038200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr14:56024400-56039000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr14:56024400-56039400	Weak transcription	Brain Angular Gyrus	brain
10	chr14:56024400-56039400	Weak transcription	Fetal Stomach	stomach
11	chr14:56024400-56039600	Weak transcription	Pancreas	Pancrea
12	chr14:56024400-56043200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:56024400-56043600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:56024400-56043600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr14:56024400-56043600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr14:56024400-56045200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr14:56024400-56045200	Weak transcription	Ovary	ovary
18	chr14:56024400-56045400	Weak transcription	Hela-S3	cervix
19	chr14:56024400-56045400	Weak transcription	Osteobl	bone
20	chr14:56024400-56045800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr14:56024600-56043800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr14:56024600-56045400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr14:56025000-56037000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr14:56025200-56045600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr14:56025800-56045400	Weak transcription	Fetal Muscle Leg	muscle
26	chr14:56026000-56043000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:56026200-56045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:56027600-56032800	Weak transcription	Fetal Heart	heart
29	chr14:56027800-56039000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr14:56028000-56044600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr14:56029200-56043600	Weak transcription	HSMM	muscle

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