Variant report

Variant	rs2641358
Chromosome Location	chr3:195254869-195254870
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	chr3:195245155..195247759-chr3:195252562..195254990,2	MCF-7	breast:
2	chr3:195248669..195250318-chr3:195253064..195255485,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPP1R2-1	chr3:195254248-195256068	ucscGeneNc_uc003ftp_2

Variant related genes	Relation type
ENSG00000252620	Chromatin interaction
ENSG00000184203	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1467282	1.00[ASN][1000 genomes]
rs17847363	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641379	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686446	0.85[AMR][1000 genomes]
rs28564334	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35792292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677687	1.00[ASN][1000 genomes]
rs4677689	1.00[ASN][1000 genomes]
rs62287557	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6605336	1.00[ASN][1000 genomes]
rs6605337	1.00[ASN][1000 genomes]
rs6801044	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647318	1.00[ASN][1000 genomes]
rs823500	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823501	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823510	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823511	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823514	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823517	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823519	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823525	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823526	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs862063	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862064	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs862065	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
2	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
4	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
6	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
7	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
9	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
10	nsv878138	chr3:195057001-195477791	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
11	nsv1006229	chr3:195071421-195474751	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
12	esv2754364	chr3:195102703-195553690	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
13	esv2757028	chr3:195102787-195479748	Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
14	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer 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 miRNA target site	144 gene(s)	inside rSNPs	diseases
15	nsv432513	chr3:195121072-195478861	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
16	nsv432514	chr3:195121110-195478861	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
17	nsv432515	chr3:195121110-195528226	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
18	nsv829824	chr3:195131067-195286698	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	esv1845367	chr3:195175217-195486486	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
20	nsv1001387	chr3:195186128-195661538	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
21	esv1808194	chr3:195201080-195619882	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
22	esv1849415	chr3:195201080-195619882	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
23	esv1850702	chr3:195201080-195619882	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
24	nsv428102	chr3:195201080-195829426	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
25	nsv428430	chr3:195201080-195829426	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
26	nsv878145	chr3:195201451-195279119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
27	nsv1007617	chr3:195240812-195474751	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
28	esv2763776	chr3:195240824-195502119	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
29	nsv1010725	chr3:195249924-195459762	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195232000-195267400	Weak transcription	Aorta	Aorta
2	chr3:195232200-195262200	Weak transcription	Fetal Kidney	kidney
3	chr3:195235200-195257800	Weak transcription	Psoas Muscle	Psoas
4	chr3:195236600-195268000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:195237600-195264000	Weak transcription	NHDF-Ad	bronchial
6	chr3:195238400-195267800	Weak transcription	NH-A	brain
7	chr3:195238600-195266800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:195239000-195259800	Weak transcription	Osteobl	bone
9	chr3:195239800-195260200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:195239800-195266200	Weak transcription	Fetal Brain Male	brain
11	chr3:195240000-195255400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:195240000-195259800	Weak transcription	Right Ventricle	heart
13	chr3:195240400-195256800	Strong transcription	Hela-S3	cervix
14	chr3:195240600-195264800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:195240800-195267000	Weak transcription	Ovary	ovary
16	chr3:195241200-195264800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:195244200-195266400	Weak transcription	NHLF	lung
18	chr3:195244400-195267800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:195244400-195268000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:195244800-195259200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:195244800-195261400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:195245200-195257400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:195245800-195267800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:195246200-195267800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:195246400-195267800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:195247000-195267000	Weak transcription	Gastric	stomach
27	chr3:195248200-195267400	Weak transcription	Colonic Mucosa	Colon
28	chr3:195248600-195259800	Weak transcription	Small Intestine	intestine
29	chr3:195249200-195256200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:195249200-195256800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:195249400-195255000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr3:195249600-195255200	Strong transcription	Fetal Intestine Large	intestine
33	chr3:195249600-195256000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:195249600-195257000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:195249800-195255000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:195249800-195255200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:195249800-195255200	Strong transcription	Liver	Liver
38	chr3:195249800-195256000	Strong transcription	Fetal Intestine Small	intestine
39	chr3:195249800-195257200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:195250200-195255200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:195250200-195256200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:195250200-195257000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:195250200-195258600	Weak transcription	Spleen	Spleen
44	chr3:195250200-195266800	Weak transcription	NHEK	skin
45	chr3:195250800-195255000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:195250800-195267400	Weak transcription	HSMM	muscle
47	chr3:195251000-195256000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:195251000-195259400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:195251000-195260200	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:195251000-195264600	Weak transcription	Adipose Nuclei	Adipose

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