Variant report

Variant	rs4902482
Chromosome Location	chr14:68001781-68001782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:67902911..67909562-chr14:67998675..68002742,8	MCF-7	breast:
2	chr14:68000136..68002027-chr14:68049030..68051645,2	K562	blood:
3	chr14:67998150..68002925-chr14:68034555..68041423,8	MCF-7	breast:
4	chr14:67999015..68003161-chr14:68029425..68040471,13	MCF-7	breast:
5	chr14:67998697..68001854-chr14:68041996..68045954,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054690	Chromatin interaction
ENSG00000265993	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11158681	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11158682	0.91[CEU][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11158683	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11158684	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12434659	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2064929	0.83[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4144498	0.87[GIH][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap]
rs4902478	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4902479	0.84[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4902483	0.92[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.97[EUR][1000 genomes]
rs4902484	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4902486	0.89[EUR][1000 genomes]
rs6573780	0.83[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7147529	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7154636	0.85[EUR][1000 genomes]
rs7155887	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs731681	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs753683	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4902482	PLEKHH1	cis	cerebellum	SCAN
rs4902482	C14orf181	cis	cerebellum	SCAN
rs4902482	ADAM20	cis	cerebellum	SCAN
rs4902482	FUT8	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67999400-68001800	Active TSS	Brain Angular Gyrus	brain
2	chr14:67999400-68002200	Active TSS	Brain Substantia Nigra	brain
3	chr14:67999400-68002600	Active TSS	Brain Anterior Caudate	brain
4	chr14:67999400-68002600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr14:67999600-68002400	Active TSS	Brain Cingulate Gyrus	brain
6	chr14:67999600-68002400	Active TSS	Brain Hippocampus Middle	brain
7	chr14:67999800-68002200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr14:68000400-68044000	Weak transcription	Spleen	Spleen
9	chr14:68000600-68002800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr14:68000600-68005200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr14:68000600-68007000	Weak transcription	Lung	lung
12	chr14:68000800-68002000	Enhancers	Fetal Brain Male	brain
13	chr14:68000800-68002200	Weak transcription	Pancreas	Pancrea
14	chr14:68000800-68004200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr14:68000800-68004800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr14:68000800-68005000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr14:68000800-68005000	Weak transcription	Adipose Nuclei	Adipose
18	chr14:68000800-68005000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr14:68000800-68005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:68000800-68011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr14:68000800-68013000	Weak transcription	A549	lung
22	chr14:68001000-68004400	Weak transcription	HMEC	breast
23	chr14:68001000-68004800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr14:68001000-68004800	Weak transcription	NHEK	skin
25	chr14:68001000-68005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:68001000-68005200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr14:68001000-68005200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr14:68001000-68005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr14:68001000-68005400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr14:68001000-68005800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr14:68001000-68007600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr14:68001000-68008000	Weak transcription	K562	blood
33	chr14:68001000-68010600	Weak transcription	Hela-S3	cervix
34	chr14:68001000-68024400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr14:68001200-68002000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr14:68001200-68002400	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr14:68001200-68002800	Weak transcription	Fetal Kidney	kidney
38	chr14:68001200-68002800	Weak transcription	Placenta	Placenta
39	chr14:68001200-68004400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr14:68001200-68004600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr14:68001200-68005000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr14:68001200-68007400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr14:68001400-68001800	Enhancers	Fetal Intestine Large	intestine
44	chr14:68001400-68001800	Enhancers	HepG2	liver
45	chr14:68001400-68002000	Enhancers	Fetal Intestine Small	intestine
46	chr14:68001400-68005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr14:68001400-68007600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr14:68001400-68028400	Weak transcription	Brain Germinal Matrix	brain
49	chr14:68001600-68001800	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr14:68001600-68002000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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