Variant report

Variant	rs72499625
Chromosome Location	chr3:194932821-194932822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr3:194932395-194932945	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194931478..194933050-chr3:194933815..194935477,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-25P	TF binding region
XXYLT1	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11918143	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919965	0.85[ASN][1000 genomes]
rs11921174	0.85[ASN][1000 genomes]
rs11928199	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12485800	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12486636	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12488616	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491426	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491902	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12493888	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12495659	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497444	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12497906	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12498063	0.85[ASN][1000 genomes]
rs35899174	0.85[ASN][1000 genomes]
rs3796161	0.82[AMR][1000 genomes]
rs56281422	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56835677	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58113840	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60677730	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61022222	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66510151	0.90[EUR][1000 genomes]
rs67413252	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67484513	0.90[EUR][1000 genomes]
rs6777904	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6790425	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6804467	0.85[ASN][1000 genomes]
rs72499624	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72607893	0.80[ASN][1000 genomes]
rs755202	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
4	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking 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	21 gene(s)	inside rSNPs	diseases
15	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	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
18	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

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194918800-194945000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:194919400-194945200	Weak transcription	Thymus	Thymus
3	chr3:194921000-194941600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:194926400-194942600	Weak transcription	Small Intestine	intestine
5	chr3:194926400-194947600	Weak transcription	Gastric	stomach
6	chr3:194926600-194933400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:194926600-194942800	Weak transcription	Hela-S3	cervix
8	chr3:194928600-194933600	Enhancers	Lung	lung
9	chr3:194929800-194947400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:194931200-194933000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:194931200-194933200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:194931200-194933400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:194931200-194934400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:194931200-194934600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:194931200-194934800	Weak transcription	Fetal Brain Female	brain
16	chr3:194931200-194935200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:194931200-194940000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:194931200-194942000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:194931200-194948800	Weak transcription	Fetal Intestine Large	intestine
20	chr3:194931400-194942000	Weak transcription	Brain Anterior Caudate	brain
21	chr3:194931400-194945400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:194931600-194933800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:194931600-194934600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:194931600-194934600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:194931600-194942000	Weak transcription	Brain Substantia Nigra	brain
26	chr3:194931600-194946600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:194931600-194958800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:194931800-194934400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:194931800-194934400	Weak transcription	Placenta	Placenta
30	chr3:194931800-194934600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:194931800-194934600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:194931800-194934800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:194931800-194935200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:194931800-194935400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:194931800-194940200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:194931800-194940600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:194931800-194941600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:194931800-194941800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:194931800-194942000	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:194931800-194944200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:194931800-194945200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr3:194931800-194956600	Weak transcription	K562	blood
43	chr3:194932000-194934800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:194932000-194940000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:194932000-194941200	Weak transcription	Esophagus	oesophagus
46	chr3:194932200-194933400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:194932200-194935000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:194932200-194940200	Weak transcription	Fetal Lung	lung
49	chr3:194932400-194933400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:194932400-194933600	Enhancers	Spleen	Spleen

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