Variant report

Variant	rs4884235
Chromosome Location	chr13:53259757-53259758
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:53258383..53260639-chr13:53264833..53266950,2	MCF-7	breast:
2	chr13:53225756..53229849-chr13:53255678..53259863,4	K562	blood:
3	chr13:53258335..53260690-chr13:53267146..53270145,2	K562	blood:

Variant related genes	Relation type
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1057478	0.85[CHB][hapmap]
rs11616261	0.84[ASN][1000 genomes]
rs11616459	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1924036	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2038826	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147692	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2575960	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs342768	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs342770	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs342778	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3742297	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4284531	0.85[CHB][hapmap]
rs616969	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6561671	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6561675	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7139495	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7139630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7324427	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7328729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7334137	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7334677	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336771	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7337021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7399901	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7997186	0.83[ASN][1000 genomes]
rs7999849	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526951	0.84[ASN][1000 genomes]
rs9526968	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9526974	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526975	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9526982	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9536104	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9536123	0.85[CEU][hapmap]
rs9536197	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9536200	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536202	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9536211	0.92[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs9536212	0.92[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs9536217	0.89[ASN][1000 genomes]
rs9536219	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9536220	0.83[CHB][hapmap]
rs9536223	0.88[ASN][1000 genomes]
rs9536236	0.92[ASN][1000 genomes]
rs9536247	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9536262	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9563113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9563114	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568750	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568751	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv900088	chr13:53250839-53274936	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53227800-53260000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:53229000-53276600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr13:53229200-53268000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr13:53230200-53263600	Weak transcription	Stomach Mucosa	stomach
5	chr13:53230400-53266400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:53230600-53266400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr13:53230800-53277400	Weak transcription	Gastric	stomach
8	chr13:53231200-53262400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr13:53231800-53266400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr13:53235200-53276000	Weak transcription	Right Ventricle	heart
11	chr13:53237200-53261800	Weak transcription	Fetal Brain Male	brain
12	chr13:53239200-53265600	Weak transcription	Brain Angular Gyrus	brain
13	chr13:53240600-53264200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:53240600-53275800	Weak transcription	K562	blood
15	chr13:53242800-53278600	Weak transcription	Psoas Muscle	Psoas
16	chr13:53245400-53263800	Strong transcription	Dnd41	blood
17	chr13:53245600-53263600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr13:53248400-53265200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr13:53248600-53263400	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr13:53248600-53265200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr13:53249000-53263400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr13:53249000-53263400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr13:53249000-53263600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr13:53249000-53266400	Strong transcription	Liver	Liver
25	chr13:53249000-53266400	Strong transcription	Fetal Intestine Large	intestine
26	chr13:53249000-53266600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr13:53249000-53267400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:53249200-53261000	Strong transcription	Adipose Nuclei	Adipose
29	chr13:53249200-53263400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr13:53249200-53265200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:53249600-53262800	Strong transcription	Fetal Thymus	thymus
32	chr13:53249800-53266000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr13:53250000-53263800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr13:53250000-53265000	Weak transcription	Hela-S3	cervix
35	chr13:53250400-53262400	Strong transcription	Placenta	Placenta
36	chr13:53250400-53263400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr13:53250600-53260000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr13:53250600-53260600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr13:53250600-53263400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:53250800-53266600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:53251000-53263600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr13:53251400-53267400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr13:53252400-53263000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:53253200-53260600	Strong transcription	HSMMtube	muscle
45	chr13:53253800-53263800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr13:53254200-53275800	Weak transcription	Fetal Heart	heart
47	chr13:53254400-53260400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:53254400-53260800	Strong transcription	Fetal Muscle Leg	muscle
49	chr13:53254800-53273600	Weak transcription	Fetal Kidney	kidney
50	chr13:53255800-53273800	Weak transcription	A549	lung

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