Variant report

Variant	rs12513891
Chromosome Location	chr5:115212818-115212819
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115175467..115180084-chr5:115209900..115212973,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145782	Chromatin interaction
ENSG00000177879	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10039749	0.94[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs10050876	0.85[ASN][1000 genomes]
rs1058600	0.81[ASN][1000 genomes]
rs10751460	1.00[ASN][1000 genomes]
rs11241336	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11241337	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12188972	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12332653	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12514553	0.98[ASN][1000 genomes]
rs12517882	0.99[ASN][1000 genomes]
rs12519850	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12520442	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12523122	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13157716	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13179199	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13361489	0.97[ASN][1000 genomes]
rs152368	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs152369	0.96[ASN][1000 genomes]
rs152397	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs152398	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs171809	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2080902	0.99[ASN][1000 genomes]
rs26529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs26536	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs26537	0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs26538	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35179959	0.81[ASN][1000 genomes]
rs35238578	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35501287	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36083750	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3733902	0.81[CHB][hapmap]
rs3756555	0.82[CHB][hapmap]
rs3797564	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs3797565	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797566	0.81[CHB][hapmap]
rs3797567	0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs3797568	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3797569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797570	0.80[ASN][1000 genomes]
rs41332950	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4143542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58463583	0.85[ASN][1000 genomes]
rs59750231	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61381571	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879485	0.99[ASN][1000 genomes]
rs6880372	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6880889	0.80[ASN][1000 genomes]
rs71581217	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7707539	1.00[ASN][1000 genomes]
rs7713314	0.98[ASN][1000 genomes]
rs7723291	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv3401617	chr5:115205732-115238678	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv3368162	chr5:115205767-115230833	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv515611	chr5:115208843-115428381	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115185600-115218600	Weak transcription	Lung	lung
2	chr5:115189800-115218600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:115189800-115235800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:115191000-115223000	Weak transcription	Right Ventricle	heart
5	chr5:115193200-115239000	Weak transcription	Gastric	stomach
6	chr5:115193600-115234600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:115194400-115218000	Weak transcription	Fetal Intestine Small	intestine
8	chr5:115194400-115220800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:115195400-115263200	Weak transcription	Aorta	Aorta
10	chr5:115195600-115214600	Weak transcription	HSMMtube	muscle
11	chr5:115196000-115233600	Weak transcription	Esophagus	oesophagus
12	chr5:115200400-115218200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:115200600-115213800	Weak transcription	Fetal Heart	heart
14	chr5:115200800-115221000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:115201000-115218200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:115202000-115218000	Weak transcription	Fetal Stomach	stomach
17	chr5:115203000-115218000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:115203400-115233400	Weak transcription	Fetal Brain Male	brain
19	chr5:115203800-115213000	Weak transcription	NHEK	skin
20	chr5:115204200-115213000	Weak transcription	Brain Germinal Matrix	brain
21	chr5:115205000-115218200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:115205000-115221600	Weak transcription	Spleen	Spleen
23	chr5:115205200-115213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:115205400-115220600	Weak transcription	Stomach Mucosa	stomach
25	chr5:115205600-115254200	Weak transcription	Small Intestine	intestine
26	chr5:115205800-115221400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:115206400-115218200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:115206800-115218200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:115207000-115218000	Weak transcription	Placenta	Placenta
30	chr5:115207000-115218200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:115207200-115213600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:115207200-115215200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:115207200-115222600	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:115207600-115218400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:115207600-115220800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr5:115207600-115233600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:115207600-115238400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:115207600-115239200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:115207600-115244600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:115207600-115253800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:115207600-115254600	Weak transcription	Fetal Kidney	kidney
42	chr5:115207800-115218000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:115207800-115218000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:115207800-115227400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr5:115207800-115250800	Weak transcription	Adipose Nuclei	Adipose
46	chr5:115207800-115254000	Weak transcription	Colon Smooth Muscle	Colon
47	chr5:115208000-115213000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:115208000-115213800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr5:115208000-115214000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:115208000-115214200	Weak transcription	Fetal Brain Female	brain

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