Variant report

Variant	rs11707272
Chromosome Location	chr3:47519606-47519607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47519409..47523186-chr3:47555017..47557218,3	K562	blood:
2	chr3:47519490..47521448-chr3:47532935..47535413,2	K562	blood:
3	chr3:47514858..47522453-chr3:47552535..47558710,16	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN23-3	chr3:47519182-47520065	NONHSAT089508

Variant related genes	Relation type
ENSG00000163832	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1024036	1.00[EUR][1000 genomes]
rs1038393	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs10865947	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1091068	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12491029	1.00[YRI][hapmap]
rs12631697	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13077134	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs1531874	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1872165	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2170814	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs295431	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs448018	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858812	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858823	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858855	1.00[AMR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6442066	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6442068	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs648226	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6772449	1.00[EUR][1000 genomes]
rs6778673	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6778687	1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787210	1.00[EUR][1000 genomes]
rs6788978	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789730	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6801270	0.84[AFR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs7372780	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612191	0.87[AMR][1000 genomes]
rs7621853	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7639121	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	1.00[EUR][1000 genomes]
rs807930	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs900688	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900689	0.94[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900690	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900693	0.90[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs900694	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs924009	1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9828124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9859947	1.00[MEX][hapmap]
rs9861247	1.00[EUR][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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47517400-47523000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:47517600-47523000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:47517800-47520600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:47517800-47523000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:47517800-47527200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:47517800-47535200	Weak transcription	Esophagus	oesophagus
7	chr3:47517800-47536600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:47517800-47544400	Weak transcription	Small Intestine	intestine
9	chr3:47518000-47520600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:47518000-47520800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:47518000-47522000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:47518000-47523000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:47518000-47523000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:47518200-47520600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:47518200-47523000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:47518200-47536600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr3:47518200-47541600	Weak transcription	Fetal Kidney	kidney
18	chr3:47518400-47520200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:47518400-47520600	Weak transcription	Fetal Intestine Large	intestine
20	chr3:47518400-47528200	Weak transcription	Fetal Brain Female	brain
21	chr3:47518400-47528200	Weak transcription	HSMM	muscle
22	chr3:47518400-47529200	Weak transcription	Fetal Stomach	stomach
23	chr3:47518400-47530000	Weak transcription	Brain Germinal Matrix	brain
24	chr3:47518400-47530600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:47518400-47532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:47518400-47535200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:47518400-47535600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:47518400-47536600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:47518400-47536600	Weak transcription	Primary T cells from cord blood	blood
30	chr3:47518400-47536600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:47518400-47536600	Weak transcription	Aorta	Aorta
32	chr3:47518400-47536600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:47518400-47536600	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:47518400-47536600	Weak transcription	Gastric	stomach
35	chr3:47518400-47536600	Weak transcription	HSMMtube	muscle
36	chr3:47518400-47536600	Weak transcription	NHLF	lung
37	chr3:47518400-47536800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:47518400-47536800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:47518400-47537000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:47518400-47539400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:47518600-47520600	Weak transcription	Fetal Intestine Small	intestine
42	chr3:47518600-47520600	Enhancers	K562	blood
43	chr3:47518600-47523200	Weak transcription	Ovary	ovary
44	chr3:47518600-47523400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:47518600-47527200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:47518600-47527200	Weak transcription	Thymus	Thymus
47	chr3:47518600-47530000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:47518600-47530000	Weak transcription	Fetal Thymus	thymus
49	chr3:47518600-47532200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:47518600-47532200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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