Variant report

Variant	rs17787211
Chromosome Location	chr3:23902733-23902734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23902696..23905210-chr3:23958576..23960216,2	MCF-7	breast:
2	chr3:23874649..23878257-chr3:23899567..23903129,3	MCF-7	breast:
3	chr3:23900524..23903496-chr3:23949527..23951902,2	K562	blood:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10865790	0.85[CHB][hapmap]
rs1133926	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1136155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11706297	0.81[ASN][1000 genomes]
rs11710647	0.81[ASN][1000 genomes]
rs11710679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711073	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11711380	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713246	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11718625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11922577	0.82[JPT][hapmap]
rs12497944	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13314607	0.84[ASN][1000 genomes]
rs13318927	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13325754	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1397880	0.81[ASN][1000 genomes]
rs1567581	0.84[ASN][1000 genomes]
rs2361013	0.81[ASN][1000 genomes]
rs28522849	0.81[ASN][1000 genomes]
rs28623591	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34476593	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35711415	0.84[ASN][1000 genomes]
rs35886023	0.81[ASN][1000 genomes]
rs4131864	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs61294694	0.81[ASN][1000 genomes]
rs61645368	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253361	0.84[ASN][1000 genomes]
rs62253380	0.84[ASN][1000 genomes]
rs62253382	0.84[ASN][1000 genomes]
rs6550809	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6765292	1.00[CHB][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs6768429	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6778970	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787216	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6789983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6800407	0.93[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72627066	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73825116	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73825124	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73825170	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73825178	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73825181	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7615238	0.84[AFR][1000 genomes]
rs7629325	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7637968	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs938078	0.81[ASN][1000 genomes]
rs9815334	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834166	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9836860	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836970	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9838694	0.84[ASN][1000 genomes]
rs9850255	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9857442	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9863674	0.84[ASN][1000 genomes]
rs9875213	0.84[ASN][1000 genomes]
rs9876561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17787211	NR1D2	cis	Temporal Cortex	GTEx
rs17787211	NR1D2	Cis_1M	lymphoblastoid	RTeQTL
rs17787211	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23876800-23906800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:23879000-23907400	Weak transcription	K562	blood
3	chr3:23882200-23905600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:23882800-23906000	Weak transcription	HepG2	liver
5	chr3:23890600-23902800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:23893600-23906400	Weak transcription	Aorta	Aorta
7	chr3:23893600-23906600	Weak transcription	Colonic Mucosa	Colon
8	chr3:23894400-23903000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:23894600-23903000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:23894800-23902800	Weak transcription	Fetal Intestine Small	intestine
11	chr3:23895000-23903400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:23898000-23904800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:23898200-23907000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:23898400-23907200	Weak transcription	Stomach Mucosa	stomach
15	chr3:23898600-23903000	Weak transcription	Fetal Stomach	stomach
16	chr3:23899000-23907000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:23899200-23902800	Enhancers	Primary hematopoietic stem cells	blood
18	chr3:23899400-23905600	Weak transcription	Liver	Liver
19	chr3:23899400-23906200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:23899400-23906200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:23899400-23907000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:23899400-23907200	Weak transcription	NH-A	brain
23	chr3:23900400-23903400	Enhancers	Brain Substantia Nigra	brain
24	chr3:23900400-23903400	Enhancers	Fetal Heart	heart
25	chr3:23900800-23903000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:23900800-23906200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:23900800-23906200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:23900800-23907000	Weak transcription	Fetal Kidney	kidney
29	chr3:23901000-23902800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:23901000-23902800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:23901000-23903000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:23901000-23903000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:23901000-23903000	Weak transcription	Fetal Lung	lung
34	chr3:23901000-23903200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr3:23901000-23903600	Weak transcription	A549	lung
36	chr3:23901000-23903600	Weak transcription	HUVEC	blood vessel
37	chr3:23901000-23905400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:23901000-23905600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:23901000-23905600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:23901000-23906000	Weak transcription	NHLF	lung
41	chr3:23901000-23906400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:23901000-23906800	Weak transcription	NHDF-Ad	bronchial
43	chr3:23901000-23907400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:23901200-23902800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:23901200-23902800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:23901200-23902800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:23901200-23902800	Weak transcription	Esophagus	oesophagus
48	chr3:23901200-23903000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:23901200-23903000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:23901200-23903600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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