Variant report

Variant	rs2586946
Chromosome Location	chr2:55851798-55851799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55843280..55846696-chr2:55847912..55852861,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1037508	0.82[ASN][1000 genomes]
rs1045910	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12463766	0.82[ASN][1000 genomes]
rs12617829	0.83[ASN][1000 genomes]
rs12619756	0.94[ASN][1000 genomes]
rs12713301	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12989898	0.87[ASN][1000 genomes]
rs13016772	0.84[ASN][1000 genomes]
rs13028892	0.83[ASN][1000 genomes]
rs13427693	0.80[EUR][1000 genomes]
rs13430657	0.80[EUR][1000 genomes]
rs1373228	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563201	0.93[ASN][1000 genomes]
rs1814457	0.90[ASN][1000 genomes]
rs1975485	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1975486	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2168097	0.92[ASN][1000 genomes]
rs2586948	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586949	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2586951	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2586955	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2586958	0.81[ASN][1000 genomes]
rs2586959	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2586960	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2586961	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2586965	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627758	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627763	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627771	0.81[ASN][1000 genomes]
rs2627774	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2627778	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2627783	0.87[ASN][1000 genomes]
rs3748945	0.84[ASN][1000 genomes]
rs3816489	0.83[ASN][1000 genomes]
rs4233962	0.82[ASN][1000 genomes]
rs4671248	0.84[ASN][1000 genomes]
rs61475257	0.87[ASN][1000 genomes]
rs62165178	0.83[ASN][1000 genomes]
rs6545505	0.94[ASN][1000 genomes]
rs6731927	0.93[ASN][1000 genomes]
rs706549	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs706550	0.82[ASN][1000 genomes]
rs706551	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs730884	0.89[ASN][1000 genomes]
rs744514	0.89[ASN][1000 genomes]
rs7559307	0.86[ASN][1000 genomes]
rs7585484	0.92[ASN][1000 genomes]
rs7605486	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7605504	0.92[ASN][1000 genomes]
rs782569	0.86[ASN][1000 genomes]
rs782570	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782571	0.83[AFR][1000 genomes]
rs782574	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782575	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782576	0.83[ASN][1000 genomes]
rs782577	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782580	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782582	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782583	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782589	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782591	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782593	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782597	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs782598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782603	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782604	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782612	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782614	0.86[ASN][1000 genomes]
rs782615	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782617	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782618	0.83[ASN][1000 genomes]
rs782620	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782621	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782623	0.81[ASN][1000 genomes]
rs782624	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782625	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782626	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782627	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782628	0.83[ASN][1000 genomes]
rs782631	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782635	0.83[ASN][1000 genomes]
rs782636	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782638	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782643	0.81[ASN][1000 genomes]
rs782647	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782648	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs782651	0.94[ASN][1000 genomes]
rs9636439	0.88[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2586946	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
8	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:55846800-55853000	Weak transcription	A549	lung
11	chr2:55846800-55858200	Weak transcription	HSMM	muscle
12	chr2:55846800-55862000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:55846800-55862000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:55846800-55862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:55846800-55862600	Weak transcription	NHDF-Ad	bronchial
16	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
17	chr2:55846800-55863400	Weak transcription	NHLF	lung
18	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:55847000-55852600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr2:55847400-55852400	Weak transcription	HMEC	breast
22	chr2:55847400-55852800	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr2:55847400-55859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:55847400-55862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:55847600-55852400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:55847600-55852600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:55847600-55852600	Weak transcription	Right Atrium	heart
29	chr2:55847600-55857400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:55847600-55860800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:55847600-55862000	Weak transcription	Osteobl	bone
32	chr2:55847600-55864200	Weak transcription	Brain Germinal Matrix	brain
33	chr2:55847600-55870000	Weak transcription	Colonic Mucosa	Colon
34	chr2:55847600-55870000	Weak transcription	Psoas Muscle	Psoas
35	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
36	chr2:55847800-55852400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:55847800-55852400	Weak transcription	NHEK	skin
38	chr2:55847800-55852600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:55847800-55859000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:55847800-55862000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:55847800-55862000	Weak transcription	NH-A	brain
42	chr2:55847800-55862200	Weak transcription	HUVEC	blood vessel
43	chr2:55847800-55863400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:55848000-55853200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:55848000-55856800	Weak transcription	Brain Angular Gyrus	brain
46	chr2:55848000-55862600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:55848000-55862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:55848000-55872600	Weak transcription	Small Intestine	intestine
49	chr2:55848600-55852400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:55848800-55862000	Weak transcription	Hela-S3	cervix

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