Variant report

Variant	rs4493057
Chromosome Location	chr16:11919959-11919960
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:11919719..11922713-chr16:11945329..11947052,3	MCF-7	breast:
2	chr16:11918375..11921492-chr16:11938739..11940419,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171490	Chromatin interaction
ENSG00000263307	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10852340	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10852341	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11075022	0.83[EUR][1000 genomes]
rs11646545	0.87[CEU][hapmap]
rs11649405	0.85[EUR][1000 genomes]
rs2018199	0.83[CEU][hapmap];0.87[ASN][1000 genomes]
rs2075158	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2098722	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33619	0.80[CEU][hapmap]
rs33623	0.80[CEU][hapmap]
rs33631	0.80[CEU][hapmap]
rs33635	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs33655	0.80[CEU][hapmap]
rs33660	0.80[CEU][hapmap]
rs3743590	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs3971913	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40311	0.80[CEU][hapmap]
rs4429311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4561483	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs456325	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs6498250	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718081	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7198817	0.84[CEU][hapmap]
rs8052900	0.86[ASN][1000 genomes]
rs8061189	0.80[CEU][hapmap]
rs9927765	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482288	chr16:11776491-11946429	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS 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	54 gene(s)	inside rSNPs	diseases
2	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4493057	NDE1	cis	parietal	SCAN
rs4493057	TNFRSF17	cis	cerebellum	SCAN
rs4493057	GSPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11916000-11921000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr16:11916600-11928800	Weak transcription	Primary B cells from cord blood	blood
3	chr16:11918600-11922600	Weak transcription	K562	blood
4	chr16:11918600-11929600	Weak transcription	Brain Anterior Caudate	brain
5	chr16:11918600-11929800	Weak transcription	Pancreas	Pancrea
6	chr16:11918600-11930000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr16:11918600-11930200	Weak transcription	Left Ventricle	heart
8	chr16:11918600-11933600	Weak transcription	Stomach Mucosa	stomach
9	chr16:11918600-11943800	Weak transcription	Right Atrium	heart
10	chr16:11918800-11920200	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr16:11918800-11929400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr16:11918800-11930000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr16:11918800-11930000	Weak transcription	Hela-S3	cervix
14	chr16:11918800-11930200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr16:11918800-11930200	Weak transcription	Colon Smooth Muscle	Colon
16	chr16:11919000-11929600	Weak transcription	Brain Hippocampus Middle	brain
17	chr16:11919000-11929800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr16:11919000-11930000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr16:11919000-11930000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr16:11919000-11930200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr16:11919000-11930400	Weak transcription	Right Ventricle	heart
22	chr16:11919000-11931400	Weak transcription	Small Intestine	intestine
23	chr16:11919200-11929400	Weak transcription	Brain Germinal Matrix	brain
24	chr16:11919200-11930000	Weak transcription	Fetal Intestine Large	intestine
25	chr16:11919600-11920600	Enhancers	HepG2	liver
26	chr16:11919800-11922800	Active TSS	Placenta	Placenta
27	chr16:11919800-11928600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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