Variant report

Variant	rs9309268
Chromosome Location	chr2:55858187-55858188
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55857547..55860047-chr2:55862706..55864207,2	MCF-7	breast:
2	chr2:55852070..55854704-chr2:55855790..55860246,6	K562	blood:
3	chr2:55843883..55847224-chr2:55855243..55860059,7	MCF-7	breast:
4	chr2:55852037..55854671-chr2:55856374..55858421,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PNPT1-1	chr2:55858185-55858573	XLOC_002099
2	lnc-CCDC104-4	chr2:55858184-55858573	NONHSAT070801

Variant related genes	Relation type
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10172181	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10172506	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10173150	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10182131	0.88[AMR][1000 genomes]
rs10194634	0.83[AMR][1000 genomes]
rs10195281	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10200159	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10203953	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10204169	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1045920	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10496044	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11676573	0.91[EUR][1000 genomes]
rs11902712	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12615063	0.88[AMR][1000 genomes]
rs12616502	0.91[EUR][1000 genomes]
rs12616982	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12622830	0.80[EUR][1000 genomes]
rs12623625	0.88[AMR][1000 genomes]
rs12989898	0.81[AFR][1000 genomes]
rs13382187	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13383352	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13399762	0.94[AMR][1000 genomes]
rs13400946	0.88[AMR][1000 genomes]
rs13407344	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13420929	0.88[AMR][1000 genomes]
rs13428382	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13428486	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13430684	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17047094	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17047119	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2867964	0.88[AMR][1000 genomes]
rs3748955	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545507	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6545508	0.86[AFR][1000 genomes]
rs6545509	1.00[EUR][1000 genomes]
rs6545510	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545512	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6545513	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6705295	0.83[AMR][1000 genomes]
rs6712314	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6717574	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6725101	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6736996	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6739788	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745430	0.84[AFR][1000 genomes]
rs6760959	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs730884	0.83[AFR][1000 genomes]
rs736345	0.89[AFR][1000 genomes]
rs744514	0.85[AFR][1000 genomes]
rs7558127	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7567115	0.88[AMR][1000 genomes]
rs7574398	0.82[AFR][1000 genomes]
rs7575906	0.88[AMR][1000 genomes]
rs7582174	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7586115	0.88[AMR][1000 genomes]
rs7586124	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7586366	0.88[AMR][1000 genomes]
rs7594212	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7594497	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9309267	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 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	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
7	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:55846800-55858200	Weak transcription	HSMM	muscle
10	chr2:55846800-55862000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:55846800-55862000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:55846800-55862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:55846800-55862600	Weak transcription	NHDF-Ad	bronchial
14	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
15	chr2:55846800-55863400	Weak transcription	NHLF	lung
16	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:55847400-55859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:55847400-55862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:55847600-55860800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:55847600-55862000	Weak transcription	Osteobl	bone
23	chr2:55847600-55864200	Weak transcription	Brain Germinal Matrix	brain
24	chr2:55847600-55870000	Weak transcription	Colonic Mucosa	Colon
25	chr2:55847600-55870000	Weak transcription	Psoas Muscle	Psoas
26	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
27	chr2:55847800-55859000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:55847800-55862000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:55847800-55862000	Weak transcription	NH-A	brain
30	chr2:55847800-55862200	Weak transcription	HUVEC	blood vessel
31	chr2:55847800-55863400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:55848000-55862600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:55848000-55862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:55848000-55872600	Weak transcription	Small Intestine	intestine
35	chr2:55848800-55862000	Weak transcription	Hela-S3	cervix
36	chr2:55849200-55858800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:55849200-55858800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:55849200-55862800	Weak transcription	Left Ventricle	heart
39	chr2:55849200-55863600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:55849200-55865200	Weak transcription	Gastric	stomach
41	chr2:55849200-55865600	Weak transcription	Fetal Brain Female	brain
42	chr2:55849200-55867400	Weak transcription	Lung	lung
43	chr2:55849200-55868200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:55849200-55868200	Weak transcription	Right Ventricle	heart
45	chr2:55849200-55869400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:55849200-55873200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:55849400-55859400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:55849400-55859800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:55849400-55862800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:55849400-55862800	Weak transcription	Placenta	Placenta

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