Variant report

Variant	rs2544593
Chromosome Location	chr5:79711150-79711151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79702746..79708231-chr5:79708726..79712058,4	MCF-7	breast:
2	chr5:79704698..79706938-chr5:79709845..79711807,2	K562	blood:

Variant related genes	Relation type
ENSG00000039319	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10052497	0.86[EUR][1000 genomes]
rs10433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1097308	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1097309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1102116	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1103116	0.90[AMR][1000 genomes];0.97[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];0.89[YRI][hapmap];0.95[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	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[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];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs173597	0.85[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];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs174076	0.88[CHB][hapmap];0.92[ASN][1000 genomes]
rs1820119	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs185100	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs187478	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs187479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs192313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs194540	0.81[AFR][1000 genomes]
rs194541	0.92[ASN][1000 genomes]
rs2112152	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[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];0.84[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];0.84[YRI][hapmap]
rs249001	0.88[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	0.84[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	0.88[EUR][1000 genomes]
rs249021	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[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];0.93[YRI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249029	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249030	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs249031	0.95[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];0.93[YRI][hapmap]
rs249037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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];0.93[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544591	0.95[ASN][1000 genomes]
rs2544592	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544598	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544599	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544600	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544603	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544604	0.90[ASN][1000 genomes]
rs2547487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2547497	0.88[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259034	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259035	0.81[AMR][1000 genomes];0.88[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	0.88[AMR][1000 genomes];0.93[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];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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]
rs259055	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]
rs2599508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[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];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096108	0.86[AFR][1000 genomes]
rs3096111	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096112	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs394076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs394170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs399261	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs401612	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs408899	0.93[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];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs835726	0.97[ASN][1000 genomes]
rs835728	0.83[ASN][1000 genomes]
rs835729	0.97[ASN][1000 genomes]
rs835731	0.82[EUR][1000 genomes]
rs856765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs856772	0.85[ASN][1000 genomes]
rs863163	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs969567	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79704600-79717000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:79704600-79723600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:79704600-79730200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:79704600-79730200	Weak transcription	Lung	lung
5	chr5:79704600-79758000	Weak transcription	Spleen	Spleen
6	chr5:79704600-79758600	Weak transcription	Gastric	stomach
7	chr5:79704800-79711200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr5:79704800-79711200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:79704800-79731600	Weak transcription	Fetal Thymus	thymus
10	chr5:79705600-79731200	Weak transcription	Aorta	Aorta
11	chr5:79705600-79757400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:79705800-79712200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:79705800-79712800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:79705800-79713000	Weak transcription	NHEK	skin
15	chr5:79705800-79715000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:79705800-79715000	Weak transcription	Fetal Intestine Small	intestine
17	chr5:79705800-79723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:79705800-79730200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:79705800-79731400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:79705800-79731800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:79706000-79711600	Weak transcription	Psoas Muscle	Psoas
22	chr5:79706000-79712600	Weak transcription	Fetal Intestine Large	intestine
23	chr5:79706000-79717800	Weak transcription	Fetal Brain Female	brain
24	chr5:79706000-79718000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:79706000-79731400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:79706000-79731800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:79706000-79732000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:79706000-79732000	Weak transcription	NHLF	lung
29	chr5:79706200-79715600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:79706200-79717400	Weak transcription	Primary T cells from cord blood	blood
31	chr5:79706200-79722000	Weak transcription	Brain Germinal Matrix	brain
32	chr5:79706200-79722200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:79706200-79731600	Weak transcription	NHDF-Ad	bronchial
34	chr5:79706400-79712000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:79706400-79713000	Weak transcription	Brain Hippocampus Middle	brain
36	chr5:79706400-79717200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:79706400-79720000	Weak transcription	Fetal Lung	lung
38	chr5:79707800-79711800	Weak transcription	Fetal Heart	heart
39	chr5:79707800-79711800	Weak transcription	K562	blood
40	chr5:79707800-79712800	Weak transcription	HSMMtube	muscle
41	chr5:79707800-79714800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:79707800-79715200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:79707800-79731600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:79707800-79731800	Weak transcription	Brain Angular Gyrus	brain
45	chr5:79707800-79735400	Weak transcription	Hela-S3	cervix
46	chr5:79708000-79712400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:79708000-79712600	Weak transcription	Brain Substantia Nigra	brain
48	chr5:79708000-79714200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:79708000-79719600	Weak transcription	Brain Anterior Caudate	brain
50	chr5:79708000-79730200	Weak transcription	Muscle Satellite Cultured Cells	--

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