Variant report

Variant	rs41259844
Chromosome Location	chr3:195781684-195781685
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	chr3:195780311..195781988-chr3:195785896..195787974,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072274	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1004860	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1004992	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12487702	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490842	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12491771	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12493933	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300779	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906439	1.00[ASN][1000 genomes]
rs366268	0.80[ASN][1000 genomes]
rs3761716	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804138	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804141	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827556	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3933	1.00[ASN][1000 genomes]
rs406271	0.96[ASN][1000 genomes]
rs41297523	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41298087	1.00[ASN][1000 genomes]
rs41298097	1.00[ASN][1000 genomes]
rs41299394	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300427	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41301353	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419059	0.96[ASN][1000 genomes]
rs492288	1.00[ASN][1000 genomes]
rs492349	1.00[ASN][1000 genomes]
rs539816	1.00[ASN][1000 genomes]
rs557527	1.00[ASN][1000 genomes]
rs570	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60148746	0.89[ASN][1000 genomes]
rs62284053	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285381	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285382	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62285387	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62285392	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62285393	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6763092	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7645812	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	nsv471621	chr3:195417664-195795474	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv469518	chr3:195623722-195795474	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482784	chr3:195623722-195795474	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv1010395	chr3:195641908-195848264	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats 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 target site	56 gene(s)	inside rSNPs	diseases
9	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription 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 target site	87 gene(s)	inside rSNPs	diseases
10	esv1820982	chr3:195651349-195835519	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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 target site	54 gene(s)	inside rSNPs	diseases
11	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	nsv878170	chr3:195677895-195871388	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
13	nsv878171	chr3:195677895-195959924	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
15	nsv1002584	chr3:195734933-195910772	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
16	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
17	nsv878172	chr3:195751853-195831098	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
18	nsv532214	chr3:195762648-195916068	Weak transcription Strong transcription Active TSS Enhancers 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 target site	50 gene(s)	inside rSNPs	diseases
19	nsv1002065	chr3:195769609-195877692	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
20	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
21	nsv524410	chr3:195776240-195816195	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers 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
22	nsv461130	chr3:195776240-195907653	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
23	nsv593069	chr3:195776240-195907653	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 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	chr3:195771400-195804000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:195773000-195802000	Strong transcription	Dnd41	blood
3	chr3:195773200-195805200	Strong transcription	Fetal Thymus	thymus
4	chr3:195773400-195800400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:195773600-195782000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:195773600-195790200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:195774200-195785600	Strong transcription	A549	lung
8	chr3:195774200-195791400	Strong transcription	Primary B cells from cord blood	blood
9	chr3:195774200-195800200	Strong transcription	Placenta	Placenta
10	chr3:195774200-195803800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:195774200-195804800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:195774400-195784400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:195774400-195800200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:195774400-195803800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:195774600-195783200	Strong transcription	HMEC	breast
16	chr3:195774600-195789600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:195774600-195803800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:195774600-195805400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:195774800-195803000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:195774800-195803400	Strong transcription	Left Ventricle	heart
21	chr3:195775000-195782200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:195775000-195782600	Strong transcription	Liver	Liver
23	chr3:195775000-195796600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:195775000-195798800	Strong transcription	Thymus	Thymus
25	chr3:195775000-195803200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:195775000-195806600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:195775200-195784200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:195775200-195784200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:195775200-195784200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:195775200-195796600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:195775200-195802800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:195775200-195804000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:195775200-195804400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:195775400-195782200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:195775400-195784000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:195775400-195784200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr3:195775400-195797600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr3:195775400-195800400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:195775400-195802600	Strong transcription	Primary T cells from cord blood	blood
40	chr3:195775400-195802800	Strong transcription	Fetal Brain Female	brain
41	chr3:195775400-195803400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:195775400-195803800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr3:195775400-195804000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:195775400-195804000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr3:195775600-195782000	Weak transcription	Stomach Mucosa	stomach
46	chr3:195775600-195782200	Strong transcription	Fetal Intestine Large	intestine
47	chr3:195775600-195782600	Strong transcription	Adipose Nuclei	Adipose
48	chr3:195775600-195783000	Strong transcription	NHEK	skin
49	chr3:195775600-195783200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:195775600-195784000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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