Variant report

Variant	rs4290789
Chromosome Location	chr3:17048715-17048716
allele	A/G
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	NFIC	chr3:17048564-17049065	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:17046166..17048957-chr3:17050812..17052932,2	MCF-7	breast:

Variant related genes	Relation type
PLCL2	TF binding region
ENSG00000154822	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12054464	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12233493	0.97[ASN][1000 genomes]
rs12233538	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233541	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066204	0.84[EUR][1000 genomes]
rs13073804	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13083189	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085309	0.85[EUR][1000 genomes]
rs13096536	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1550518	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17042972	0.87[ASN][1000 genomes]
rs17200543	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17272740	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17272810	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17272817	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17272831	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28498854	0.95[EUR][1000 genomes]
rs28932173	0.93[ASN][1000 genomes]
rs34053933	0.88[EUR][1000 genomes]
rs34126040	0.81[EUR][1000 genomes]
rs34437014	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34824028	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35100600	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35307172	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3935970	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55942882	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56060350	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58855245	0.88[EUR][1000 genomes]
rs59256854	0.88[EUR][1000 genomes]
rs62246031	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62247182	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789069	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6796868	0.90[ASN][1000 genomes]
rs71627166	0.87[EUR][1000 genomes]
rs7616589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652293	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7652874	0.85[EUR][1000 genomes]
rs9815788	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834723	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835432	0.87[EUR][1000 genomes]
rs9845137	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858664	0.90[ASN][1000 genomes]
rs9876768	0.93[EUR][1000 genomes]

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17037000-17053200	Weak transcription	Fetal Intestine Small	intestine
2	chr3:17037600-17050800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:17040200-17051000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:17040200-17051200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr3:17041200-17051400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:17043800-17048800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr3:17044000-17048800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:17044000-17050800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:17044600-17049000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:17044800-17048800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:17045000-17053800	Weak transcription	Thymus	Thymus
12	chr3:17045200-17050000	Weak transcription	Lung	lung
13	chr3:17045200-17052200	Weak transcription	Aorta	Aorta
14	chr3:17045400-17051200	Weak transcription	Placenta	Placenta
15	chr3:17046200-17049600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr3:17046200-17053200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:17046600-17050000	Enhancers	Primary T cells from cord blood	blood
18	chr3:17046600-17053000	Weak transcription	Brain Substantia Nigra	brain
19	chr3:17046800-17054200	Weak transcription	Psoas Muscle	Psoas
20	chr3:17046800-17054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:17047000-17051800	Weak transcription	Fetal Brain Female	brain
22	chr3:17047000-17054200	Weak transcription	Brain Anterior Caudate	brain
23	chr3:17047800-17048800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr3:17047800-17048800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:17047800-17050000	Enhancers	GM12878-XiMat	blood
26	chr3:17048000-17050800	Weak transcription	Primary B cells from cord blood	blood
27	chr3:17048000-17051400	Weak transcription	Fetal Lung	lung
28	chr3:17048000-17051400	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:17048000-17051600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:17048000-17052600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:17048200-17049400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:17048200-17051200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:17048200-17051200	Weak transcription	Fetal Thymus	thymus
34	chr3:17048200-17051200	Weak transcription	Left Ventricle	heart
35	chr3:17048200-17051200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:17048200-17051200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:17048200-17051200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:17048200-17051400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:17048200-17051400	Weak transcription	Adipose Nuclei	Adipose
40	chr3:17048200-17051600	Weak transcription	Fetal Kidney	kidney
41	chr3:17048200-17052000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:17048200-17052400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:17048200-17052600	Weak transcription	Spleen	Spleen
44	chr3:17048200-17053000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:17048200-17053000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:17048200-17053200	Weak transcription	Liver	Liver
47	chr3:17048200-17053200	Weak transcription	Stomach Mucosa	stomach
48	chr3:17048200-17054200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:17048200-17054600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:17048200-17054600	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links