Variant report

Variant	rs6442066
Chromosome Location	chr3:47456225-47456226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47439793..47442419-chr3:47454584..47456285,2	K562	blood:
2	chr3:47451769..47453360-chr3:47455312..47457238,2	MCF-7	breast:
3	chr3:47421651..47424349-chr3:47455867..47459560,4	MCF-7	breast:
4	chr3:47454820..47460433-chr3:47460723..47465409,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN23-1	chr3:47456053-47457107	NONHSAT089499
2	lnc-PTPN23-1	chr3:47456053-47457105	ENSG00000250823

Variant related genes	Relation type
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000114650	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1024036	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1038393	1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs10865947	1.00[EUR][1000 genomes]
rs1091068	1.00[EUR][1000 genomes]
rs11707272	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11711725	0.89[YRI][hapmap]
rs11922925	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12631697	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13077134	1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1531874	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1809487	1.00[AMR][1000 genomes]
rs1872165	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs295431	1.00[EUR][1000 genomes]
rs295432	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs295434	1.00[EUR][1000 genomes]
rs295443	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	1.00[EUR][1000 genomes]
rs295450	1.00[EUR][1000 genomes]
rs295451	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs295453	1.00[EUR][1000 genomes]
rs295454	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs295455	1.00[EUR][1000 genomes]
rs295456	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs295457	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs295459	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs448018	1.00[EUR][1000 genomes]
rs4858812	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4858823	1.00[EUR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs55736379	1.00[AMR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6442068	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6442069	1.00[EUR][1000 genomes]
rs648226	1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6772449	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6778673	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6778687	1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	1.00[EUR][1000 genomes]
rs6787210	1.00[EUR][1000 genomes]
rs6788978	1.00[EUR][1000 genomes]
rs6789730	1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs7372780	1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs73831515	1.00[AMR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7639121	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7649413	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs807930	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs869508	0.82[YRI][hapmap]
rs900688	1.00[EUR][1000 genomes]
rs900689	1.00[EUR][1000 genomes]
rs900690	1.00[EUR][1000 genomes]
rs900691	0.87[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900692	1.00[EUR][1000 genomes]
rs900693	1.00[TSI][hapmap]
rs900694	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs924009	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9828124	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9869489	1.00[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	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
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47426200-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:47436200-47462000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:47437800-47462800	Weak transcription	Fetal Brain Male	brain
4	chr3:47441000-47476800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:47441400-47462400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:47444800-47459400	Strong transcription	Liver	Liver
7	chr3:47445000-47462000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:47445000-47462400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:47445000-47462800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:47445600-47462800	Strong transcription	Fetal Brain Female	brain
11	chr3:47446000-47458400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:47446000-47462200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:47446000-47462800	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:47446200-47462000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:47446200-47462800	Strong transcription	Dnd41	blood
16	chr3:47446400-47462800	Strong transcription	Colonic Mucosa	Colon
17	chr3:47446600-47457400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:47446600-47462800	Strong transcription	Brain Germinal Matrix	brain
19	chr3:47446800-47459400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:47446800-47462000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:47446800-47462200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr3:47447000-47462400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:47447000-47462400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:47447000-47462400	Weak transcription	Fetal Heart	heart
25	chr3:47447000-47462400	Strong transcription	NHLF	lung
26	chr3:47447000-47462600	Strong transcription	Fetal Stomach	stomach
27	chr3:47447200-47457400	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr3:47447200-47462200	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:47447200-47462400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:47447400-47457400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:47447400-47462200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:47447400-47462400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr3:47447400-47462600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:47447600-47458800	Strong transcription	Rectal Smooth Muscle	rectum
35	chr3:47447600-47459000	Strong transcription	Colon Smooth Muscle	Colon
36	chr3:47447600-47459200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:47447800-47456400	Strong transcription	Small Intestine	intestine
38	chr3:47447800-47462400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:47447800-47462400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:47447800-47462400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr3:47447800-47462600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:47447800-47462800	Weak transcription	Right Atrium	heart
43	chr3:47448000-47457200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr3:47448000-47457200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:47448000-47461800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:47448200-47457000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:47448200-47457000	Strong transcription	Aorta	Aorta
48	chr3:47448200-47457400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:47448200-47462400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:47448200-47462400	Strong transcription	Left Ventricle	heart

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