Variant report

Variant	rs8007832
Chromosome Location	chr14:56035579-56035580
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	chr14:56033592..56036250-chr14:56045562..56047730,3	MCF-7	breast:
2	chr14:56029954..56032849-chr14:56033323..56035945,2	K562	blood:

Variant related genes	Relation type
ENSG00000126777	Chromatin interaction
ENSG00000186615	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10136386	0.88[CEU][hapmap]
rs10145555	0.80[EUR][1000 genomes]
rs10146870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10444721	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10483649	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs10483651	0.85[EUR][1000 genomes]
rs12432588	0.92[ASN][1000 genomes]
rs12432887	0.82[MEX][hapmap]
rs12434609	0.81[EUR][1000 genomes]
rs12587735	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs12589867	0.93[ASN][1000 genomes]
rs12590388	0.82[MEX][hapmap]
rs12882850	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12891129	0.80[EUR][1000 genomes]
rs12891526	0.87[EUR][1000 genomes]
rs12893162	0.95[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs12895366	0.80[EUR][1000 genomes]
rs12897227	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17128610	0.84[ASN][1000 genomes]
rs17128614	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs17128684	0.82[MEX][hapmap]
rs17253737	0.81[EUR][1000 genomes]
rs17684916	0.85[EUR][1000 genomes]
rs17684959	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs17685650	0.85[EUR][1000 genomes]
rs1951887	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs1951890	0.82[CHD][hapmap]
rs2093800	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296182	1.00[CEU][hapmap]
rs2296183	0.85[EUR][1000 genomes]
rs2341889	0.84[ASN][1000 genomes]
rs28581272	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34133022	0.81[EUR][1000 genomes]
rs34706911	0.87[EUR][1000 genomes]
rs34853759	0.81[EUR][1000 genomes]
rs34931260	0.84[ASN][1000 genomes]
rs34982220	0.84[EUR][1000 genomes]
rs35047443	0.82[ASN][1000 genomes]
rs35420484	0.84[ASN][1000 genomes]
rs35451981	0.84[ASN][1000 genomes]
rs35531912	0.86[ASN][1000 genomes]
rs3765515	1.00[CEU][hapmap]
rs4457912	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55760841	0.84[ASN][1000 genomes]
rs55927221	0.84[EUR][1000 genomes]
rs6573051	0.84[EUR][1000 genomes]
rs6573053	0.96[CEU][hapmap]
rs6573054	1.00[CEU][hapmap]
rs68127620	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7150285	0.87[CEU][hapmap];0.89[GIH][hapmap];0.82[EUR][1000 genomes]
rs7154548	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7158176	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs72719463	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8007183	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8008764	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8011252	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8011732	0.80[CEU][hapmap]
rs942317	0.81[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8007832	KTN1	cis	multi-tissue	Pritchard
rs8007832	CNIH	cis	cerebellum	SCAN
rs8007832	GCH1	cis	parietal	SCAN
rs8007832	KTN1	cis	parietal	SCAN
rs8007832	FBXO34	cis	parietal	SCAN
rs8007832	KTN1	cis	cerebellum	SCAN
rs8007832	GCH1	cis	cerebellum	SCAN

Chromatin state (count:34 , 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	chr14:56024400-56038200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr14:56024400-56039000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:56024400-56039400	Weak transcription	Brain Angular Gyrus	brain
8	chr14:56024400-56039400	Weak transcription	Fetal Stomach	stomach
9	chr14:56024400-56039600	Weak transcription	Pancreas	Pancrea
10	chr14:56024400-56043200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:56024400-56043600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:56024400-56043600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr14:56024400-56043600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr14:56024400-56045200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr14:56024400-56045200	Weak transcription	Ovary	ovary
16	chr14:56024400-56045400	Weak transcription	Hela-S3	cervix
17	chr14:56024400-56045400	Weak transcription	Osteobl	bone
18	chr14:56024400-56045800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr14:56024600-56043800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr14:56024600-56045400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr14:56025000-56037000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr14:56025200-56045600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr14:56025800-56045400	Weak transcription	Fetal Muscle Leg	muscle
24	chr14:56026000-56043000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr14:56026200-56045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr14:56027800-56039000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr14:56028000-56044600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr14:56029200-56043600	Weak transcription	HSMM	muscle
29	chr14:56034200-56046000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:56035000-56039600	Enhancers	Fetal Heart	heart
31	chr14:56035200-56035800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr14:56035200-56035800	Enhancers	A549	lung
33	chr14:56035200-56036000	Enhancers	HepG2	liver
34	chr14:56035400-56035600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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