Variant report

Variant	rs4672055
Chromosome Location	chr2:55797231-55797232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55793493..55797277-chr2:55842586..55846182,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10454749	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10496050	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1058582	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1084522	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11125579	0.87[EUR][1000 genomes]
rs11125581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17278044	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17369191	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17798852	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823893	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1975484	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1975487	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2054728	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2586947	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2586968	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2586969	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2586970	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2627759	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2627776	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2627777	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2627780	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2627782	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35504023	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762513	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4290693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4312532	0.92[AFR][1000 genomes]
rs4672052	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4672054	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4672056	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55761024	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58003472	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62165173	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62165181	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62165182	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62165183	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62165184	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62165196	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62165197	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62165200	0.81[AFR][1000 genomes]
rs6545506	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6739513	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7582278	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7594279	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7598650	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782586	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs782587	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782588	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs782590	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782594	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs782595	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782599	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782600	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782601	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782602	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782613	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs782649	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs782650	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs782652	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs935177	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4672055	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
4	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:55770800-55815800	Strong transcription	Liver	Liver
6	chr2:55775200-55798000	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr2:55779400-55798200	Strong transcription	Placenta	Placenta
8	chr2:55779400-55801400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:55779600-55797400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:55779600-55816200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:55780000-55801400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr2:55781600-55808800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:55782200-55797400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr2:55785000-55805000	Weak transcription	NHEK	skin
16	chr2:55787800-55797400	Weak transcription	Brain Angular Gyrus	brain
17	chr2:55788600-55816600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr2:55788800-55808200	Weak transcription	Right Ventricle	heart
19	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:55789600-55801200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:55789600-55804800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:55789800-55799800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:55789800-55802600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:55789800-55808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:55789800-55822800	Weak transcription	HSMMtube	muscle
26	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:55790200-55812800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
30	chr2:55790400-55808800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
32	chr2:55790800-55799400	Weak transcription	Hela-S3	cervix
33	chr2:55790800-55816600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:55790800-55819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:55791200-55812200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:55791400-55805800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:55792000-55804000	Weak transcription	K562	blood
38	chr2:55792000-55806000	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:55792600-55798000	Strong transcription	GM12878-XiMat	blood
40	chr2:55792600-55800200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:55792600-55800600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:55792800-55797600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:55793200-55805200	Weak transcription	NHDF-Ad	bronchial
44	chr2:55793400-55817000	Strong transcription	Fetal Thymus	thymus
45	chr2:55793600-55798000	Strong transcription	Stomach Smooth Muscle	stomach
46	chr2:55793600-55798000	Strong transcription	HepG2	liver
47	chr2:55793600-55798200	Strong transcription	Fetal Intestine Large	intestine
48	chr2:55793800-55798000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:55793800-55799000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:55793800-55799200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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