Variant report

Variant	rs4131403
Chromosome Location	chr3:23993437-23993438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:23992867-23993822	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23980180..23982144-chr3:23992758..23995198,2	K562	blood:
2	chr3:23992186..23994310-chr3:24012801..24015062,2	MCF-7	breast:

Variant related genes	Relation type
NR1D2	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11717862	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13091509	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13095392	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4025822	0.81[EUR][1000 genomes]
rs4241514	0.85[EUR][1000 genomes]
rs4241515	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4241517	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4241520	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4320034	0.84[AFR][1000 genomes]
rs4321479	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4589882	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4619734	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858094	0.83[EUR][1000 genomes]
rs4858095	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858098	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4858551	0.83[EUR][1000 genomes]
rs4858553	0.83[EUR][1000 genomes]
rs4858565	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858567	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62253379	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6419846	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6550815	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6550819	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6550823	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6550824	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6764154	0.83[EUR][1000 genomes]
rs6778783	0.85[EUR][1000 genomes]
rs6779476	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6790557	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6793391	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6794922	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7371944	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7431301	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9310725	0.83[EUR][1000 genomes]
rs9845287	0.83[EUR][1000 genomes]
rs9863320	0.81[EUR][1000 genomes]
rs9879378	0.82[EUR][1000 genomes]
rs9882735	0.97[EUR][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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988000-23995000	Weak transcription	Spleen	Spleen
2	chr3:23988200-23993800	Enhancers	Brain Substantia Nigra	brain
3	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
4	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:23988400-23993600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr3:23988400-23995200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
11	chr3:23988600-23994000	Enhancers	Psoas Muscle	Psoas
12	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:23989000-23993800	Enhancers	Liver	Liver
14	chr3:23989000-23996400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:23989000-23997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:23989000-23998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:23989200-23995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:23989200-23996000	Enhancers	Adipose Nuclei	Adipose
19	chr3:23989200-23996200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:23989200-23996200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
23	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
24	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:23989400-23993800	Enhancers	Brain Anterior Caudate	brain
28	chr3:23989400-23994400	Enhancers	Brain Angular Gyrus	brain
29	chr3:23989400-23996000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:23989400-23996200	Enhancers	Brain Hippocampus Middle	brain
31	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
33	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
34	chr3:23989800-23994600	Weak transcription	Lung	lung
35	chr3:23989800-23995600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:23989800-23996000	Weak transcription	Osteobl	bone
37	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:23990000-24000200	Weak transcription	HUVEC	blood vessel
39	chr3:23990000-24001000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:23990400-23995400	Weak transcription	Aorta	Aorta
41	chr3:23990400-23996200	Weak transcription	Placenta	Placenta
42	chr3:23990400-23997600	Weak transcription	NH-A	brain
43	chr3:23990600-23995600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr3:23990600-23999800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:23990800-23995800	Enhancers	Primary B cells from cord blood	blood
46	chr3:23991000-23993800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr3:23991000-23996000	Enhancers	Primary B cells from peripheral blood	blood
48	chr3:23991000-23996400	Enhancers	Brain Cingulate Gyrus	brain
49	chr3:23991400-23996000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:23991600-23993800	Weak transcription	Left Ventricle	heart

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