Variant report

Variant	rs7399901
Chromosome Location	chr13:53193214-53193215
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:53028109..53029845-chr13:53190052..53193351,3	MCF-7	breast:
2	chr13:53191451..53193324-chr13:53224550..53227605,3	MCF-7	breast:
3	chr13:53189348..53193688-chr13:53225267..53228139,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165416	Chromatin interaction
ENSG00000136108	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11148260	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11616261	0.90[ASN][1000 genomes]
rs11617331	0.83[ASN][1000 genomes]
rs1811894	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1811895	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2038826	0.86[ASN][1000 genomes]
rs2147676	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2147692	0.85[ASN][1000 genomes]
rs2575960	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342768	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342770	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342778	0.86[ASN][1000 genomes]
rs3742297	0.86[ASN][1000 genomes]
rs4884235	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885325	0.83[ASN][1000 genomes]
rs616969	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61958118	0.83[ASN][1000 genomes]
rs6561671	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6561675	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139495	0.87[ASN][1000 genomes]
rs7139630	0.87[ASN][1000 genomes]
rs7324427	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7328729	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7334137	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7334677	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7336771	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7337021	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7997186	0.89[ASN][1000 genomes]
rs7999849	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9526951	0.90[ASN][1000 genomes]
rs9526968	0.88[ASN][1000 genomes]
rs9526974	0.88[ASN][1000 genomes]
rs9526975	0.88[ASN][1000 genomes]
rs9526982	0.88[ASN][1000 genomes]
rs9536197	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9536200	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9536202	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9536211	0.90[ASN][1000 genomes]
rs9536212	0.90[ASN][1000 genomes]
rs9536217	0.91[ASN][1000 genomes]
rs9536219	0.90[ASN][1000 genomes]
rs9536223	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9536236	0.88[ASN][1000 genomes]
rs9536247	0.86[ASN][1000 genomes]
rs9536262	0.83[ASN][1000 genomes]
rs9563113	0.93[ASN][1000 genomes]
rs9563114	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568750	0.94[ASN][1000 genomes]
rs9568751	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[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	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv900085	chr13:53022518-53216622	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv900086	chr13:53030565-53208030	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv820041	chr13:53061338-53280588	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv900087	chr13:53119704-53208030	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv819201	chr13:53137490-53240330	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
13	nsv1037189	chr13:53173013-53287060	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv541775	chr13:53173013-53287060	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
18	nsv976119	chr13:53176029-53218496	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53192000-53224800	Weak transcription	Small Intestine	intestine
2	chr13:53192000-53225000	Weak transcription	Spleen	Spleen
3	chr13:53192200-53202200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:53192200-53202200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:53192200-53214000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr13:53192200-53224200	Weak transcription	Esophagus	oesophagus
7	chr13:53192200-53224800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:53192200-53224800	Weak transcription	Gastric	stomach
9	chr13:53192200-53224800	Weak transcription	Pancreas	Pancrea
10	chr13:53192200-53224800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr13:53192400-53193400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr13:53192400-53193600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr13:53192400-53194400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr13:53192400-53196000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr13:53192400-53196800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr13:53192400-53198000	Weak transcription	Thymus	Thymus
17	chr13:53192400-53199400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr13:53192400-53199600	Weak transcription	HSMM	muscle
19	chr13:53192400-53199800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr13:53192400-53200000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr13:53192400-53202200	Weak transcription	Fetal Intestine Large	intestine
22	chr13:53192400-53202200	Weak transcription	Fetal Intestine Small	intestine
23	chr13:53192400-53202200	Weak transcription	Left Ventricle	heart
24	chr13:53192400-53202200	Weak transcription	Lung	lung
25	chr13:53192400-53202400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr13:53192400-53202400	Weak transcription	Ovary	ovary
27	chr13:53192400-53203000	Weak transcription	Aorta	Aorta
28	chr13:53192400-53203400	Weak transcription	Brain Substantia Nigra	brain
29	chr13:53192400-53205400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr13:53192400-53206600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr13:53192400-53214200	Weak transcription	Psoas Muscle	Psoas
32	chr13:53192400-53214600	Weak transcription	Placenta	Placenta
33	chr13:53192400-53223400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr13:53192400-53224800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr13:53192400-53224800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr13:53192400-53225000	Weak transcription	Right Ventricle	heart
37	chr13:53192400-53225800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr13:53192600-53193400	Enhancers	Primary B cells from cord blood	blood
39	chr13:53192600-53193600	Enhancers	Brain Germinal Matrix	brain
40	chr13:53192600-53193600	Enhancers	Fetal Brain Female	brain
41	chr13:53192600-53194200	Weak transcription	Fetal Lung	lung
42	chr13:53192600-53196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr13:53192600-53197800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr13:53192600-53199400	Weak transcription	Fetal Muscle Leg	muscle
45	chr13:53192600-53199600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr13:53192600-53199800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr13:53192600-53200000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr13:53192600-53200200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr13:53192600-53205400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr13:53192600-53206600	Weak transcription	H1 Cell Line	embryonic stem cell

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