Variant report

Variant	rs259055
Chromosome Location	chr5:79708289-79708290
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79704087..79706169-chr5:79706671..79709625,3	MCF-7	breast:
2	chr5:79701683..79704303-chr5:79707202..79710047,3	K562	blood:
3	chr5:79704434..79706120-chr5:79706146..79708385,2	K562	blood:
4	chr5:79703202..79705263-chr5:79706563..79708626,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000039319	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10052497	0.88[EUR][1000 genomes]
rs10433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10474621	0.87[ASN][1000 genomes]
rs10942926	0.90[ASN][1000 genomes]
rs1097307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1097308	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1097309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1102116	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1103116	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1104243	0.82[ASN][1000 genomes]
rs13354660	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13359253	0.84[ASN][1000 genomes]
rs1363775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423113	0.92[ASN][1000 genomes]
rs16877755	0.87[ASN][1000 genomes]
rs16877757	0.87[ASN][1000 genomes]
rs168938	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs168940	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs171595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs171596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs171821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs173597	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs173599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs174075	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs174076	0.88[CHB][hapmap];0.92[ASN][1000 genomes]
rs1820119	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs185100	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs187478	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs187479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs192313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs194541	0.92[ASN][1000 genomes]
rs2112152	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2251759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs248995	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs248999	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs249000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs249001	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs249004	0.85[ASN][1000 genomes]
rs249005	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs249016	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs249020	0.86[EUR][1000 genomes]
rs249021	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs249024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249029	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249030	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs249031	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249032	0.85[ASN][1000 genomes]
rs249033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs249037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs249039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544591	0.95[ASN][1000 genomes]
rs2544592	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544598	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544599	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544600	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544603	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544604	0.90[ASN][1000 genomes]
rs2547487	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2547497	0.91[EUR][1000 genomes]
rs259023	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs259024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs259025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259026	1.00[ASN][1000 genomes]
rs259027	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs259028	0.86[CHB][hapmap];0.90[ASN][1000 genomes]
rs259029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs259030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs259031	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259032	0.90[ASN][1000 genomes]
rs259033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259034	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259035	0.91[EUR][1000 genomes]
rs259036	0.92[ASN][1000 genomes]
rs259037	0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs259038	0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs259039	0.95[ASN][1000 genomes]
rs259040	0.95[ASN][1000 genomes]
rs259041	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259042	0.88[CHB][hapmap];0.95[ASN][1000 genomes]
rs259043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259044	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs259045	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs259046	0.95[ASN][1000 genomes]
rs259047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs259048	0.88[CHB][hapmap];0.95[ASN][1000 genomes]
rs259049	1.00[JPT][hapmap]
rs259051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs259052	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs259053	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs259054	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2599508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28496723	0.89[ASN][1000 genomes]
rs28555465	0.89[ASN][1000 genomes]
rs3095851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096111	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096112	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs394076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs394170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs399261	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs401612	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs408899	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4704674	0.90[ASN][1000 genomes]
rs557346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6869519	0.87[ASN][1000 genomes]
rs6885891	0.92[ASN][1000 genomes]
rs6887302	1.00[JPT][hapmap]
rs701380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs835726	0.97[ASN][1000 genomes]
rs835728	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs835729	0.97[ASN][1000 genomes]
rs835731	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs856765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs856772	0.85[ASN][1000 genomes]
rs863163	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs969567	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS 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 miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv518480	chr5:79586085-79748382	Enhancers Strong transcription Weak transcription Flanking Active TSS 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	26 gene(s)	inside rSNPs	diseases
3	nsv1028027	chr5:79694699-79841752	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79704600-79710000	Weak transcription	Pancreas	Pancrea
2	chr5:79704600-79710600	Weak transcription	Small Intestine	intestine
3	chr5:79704600-79717000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:79704600-79723600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:79704600-79730200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:79704600-79730200	Weak transcription	Lung	lung
7	chr5:79704600-79758000	Weak transcription	Spleen	Spleen
8	chr5:79704600-79758600	Weak transcription	Gastric	stomach
9	chr5:79704800-79711200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr5:79704800-79711200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:79704800-79731600	Weak transcription	Fetal Thymus	thymus
12	chr5:79705600-79731200	Weak transcription	Aorta	Aorta
13	chr5:79705600-79757400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:79705800-79708400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:79705800-79708600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:79705800-79708800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:79705800-79709000	Weak transcription	Stomach Mucosa	stomach
18	chr5:79705800-79709600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:79705800-79710200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:79705800-79710400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:79705800-79712200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:79705800-79712800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:79705800-79713000	Weak transcription	NHEK	skin
24	chr5:79705800-79715000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:79705800-79715000	Weak transcription	Fetal Intestine Small	intestine
26	chr5:79705800-79723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:79705800-79730200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:79705800-79731400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:79705800-79731800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:79706000-79708800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:79706000-79709400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr5:79706000-79709400	Weak transcription	A549	lung
33	chr5:79706000-79710200	Weak transcription	Primary B cells from cord blood	blood
34	chr5:79706000-79710400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:79706000-79710800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr5:79706000-79710800	Weak transcription	HUVEC	blood vessel
37	chr5:79706000-79711600	Weak transcription	Psoas Muscle	Psoas
38	chr5:79706000-79712600	Weak transcription	Fetal Intestine Large	intestine
39	chr5:79706000-79717800	Weak transcription	Fetal Brain Female	brain
40	chr5:79706000-79718000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:79706000-79731400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr5:79706000-79731800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:79706000-79732000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:79706000-79732000	Weak transcription	NHLF	lung
45	chr5:79706200-79710200	Weak transcription	Osteobl	bone
46	chr5:79706200-79715600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:79706200-79717400	Weak transcription	Primary T cells from cord blood	blood
48	chr5:79706200-79722000	Weak transcription	Brain Germinal Matrix	brain
49	chr5:79706200-79722200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:79706200-79731600	Weak transcription	NHDF-Ad	bronchial

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