Variant report

Variant	rs9856727
Chromosome Location	chr3:23970232-23970233
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	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197885	Chromatin interaction
ENSG00000174738	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1133926	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1136155	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706297	0.90[ASN][1000 genomes]
rs11710647	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11711073	0.90[ASN][1000 genomes]
rs11711380	0.84[ASN][1000 genomes]
rs11713246	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11718625	0.84[ASN][1000 genomes]
rs12497944	0.94[ASN][1000 genomes]
rs13314607	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13318927	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13325754	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1397880	0.90[ASN][1000 genomes]
rs1567581	0.94[ASN][1000 genomes]
rs2361013	0.90[ASN][1000 genomes]
rs28522849	0.90[ASN][1000 genomes]
rs28623591	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34476593	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35711415	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35886023	0.90[ASN][1000 genomes]
rs4131864	0.94[ASN][1000 genomes]
rs60699428	0.85[ASN][1000 genomes]
rs61294694	0.90[ASN][1000 genomes]
rs62253361	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62253380	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62253382	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62253383	0.85[ASN][1000 genomes]
rs62253387	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6550809	0.84[EUR][1000 genomes]
rs6778970	0.84[EUR][1000 genomes]
rs6787216	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6789983	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6800407	0.87[EUR][1000 genomes]
rs72627066	0.86[EUR][1000 genomes]
rs73825170	0.84[ASN][1000 genomes]
rs73825178	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73825181	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629325	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8933	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs938078	0.90[ASN][1000 genomes]
rs9815334	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9834166	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9836860	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9836970	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9838694	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9850255	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9857442	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9863605	0.88[ASN][1000 genomes]
rs9863674	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875213	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876561	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9856727	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL
rs9856727	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23961800-23972800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:23961800-23980200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:23962000-23972800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:23962000-23974800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:23962000-23977800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:23962000-23985600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:23963000-23975200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:23963200-23973200	Weak transcription	GM12878-XiMat	blood
9	chr3:23963200-23976000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:23963600-23973200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:23963800-23970600	Weak transcription	Primary T cells from cord blood	blood
12	chr3:23963800-23971000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:23963800-23973000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:23963800-23978400	Weak transcription	Aorta	Aorta
15	chr3:23964000-23974600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:23964200-23985000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:23964400-23973200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:23964400-23974400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:23965800-23973800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:23966000-23970600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:23968800-23970600	Enhancers	NHEK	skin
22	chr3:23969200-23970400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr3:23969400-23970400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:23970000-23970400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr3:23970000-23970400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:23970000-23970400	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:23970000-23970400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:23970000-23970400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:23970000-23970400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:23970000-23970400	Enhancers	Hela-S3	cervix
31	chr3:23970000-23970400	Enhancers	K562	blood
32	chr3:23970000-23970600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr3:23970000-23970600	Enhancers	Fetal Thymus	thymus
34	chr3:23970200-23970400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:23970200-23970400	Enhancers	Fetal Kidney	kidney
36	chr3:23970200-23970600	Enhancers	Primary hematopoietic stem cells	blood

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