Variant report

Variant	rs4886991
Chromosome Location	chr15:78324442-78324443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78323235..78324806-chr15:78328346..78331306,2	MCF-7	breast:
2	chr15:78324279..78326557-chr15:78328484..78331455,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221476	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1053506	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10775214	1.00[YRI][hapmap]
rs10775215	1.00[ASN][1000 genomes]
rs11072725	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072726	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11633329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633569	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636889	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854102	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12595595	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898535	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900731	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901492	1.00[ASN][1000 genomes]
rs12913206	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12915731	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12915847	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916320	1.00[ASN][1000 genomes]
rs1348256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969502	1.00[CEU][hapmap]
rs17477813	0.85[YRI][hapmap]
rs1837911	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1837912	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015951	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044100	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2867984	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680277	1.00[ASN][1000 genomes]
rs3972617	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243072	1.00[ASN][1000 genomes]
rs4243073	0.82[AFR][1000 genomes]
rs4316722	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4411474	1.00[ASN][1000 genomes]
rs4886551	1.00[ASN][1000 genomes]
rs4886552	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886556	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886985	1.00[ASN][1000 genomes]
rs4886986	1.00[ASN][1000 genomes]
rs4886987	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886990	1.00[ASN][1000 genomes]
rs4886993	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886997	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886998	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887001	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887002	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887003	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4887004	1.00[ASN][1000 genomes]
rs61732053	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163997	1.00[ASN][1000 genomes]
rs7169882	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170101	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170286	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170452	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174640	1.00[CEU][hapmap]
rs7175192	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175235	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180684	1.00[JPT][hapmap]
rs8025423	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033216	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894295	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894296	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894302	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788640	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920180	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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	80 gene(s)	inside rSNPs	diseases
2	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78301400-78342200	Weak transcription	HMEC	breast
3	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:78305400-78329800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:78305600-78325800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:78308800-78327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:78309200-78330200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:78309200-78330800	Weak transcription	A549	lung
10	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:78311800-78326800	Weak transcription	K562	blood
12	chr15:78313000-78327600	Weak transcription	Fetal Brain Male	brain
13	chr15:78316000-78332400	Weak transcription	Hela-S3	cervix
14	chr15:78316200-78324600	Strong transcription	Fetal Intestine Small	intestine
15	chr15:78316200-78326200	Weak transcription	Fetal Kidney	kidney
16	chr15:78317000-78327800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:78317400-78326000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:78317400-78326200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:78317400-78342600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:78317600-78324600	Strong transcription	Liver	Liver
22	chr15:78317600-78326800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:78317600-78327000	Weak transcription	NH-A	brain
24	chr15:78317600-78327400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:78317800-78324600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr15:78317800-78326400	Weak transcription	Gastric	stomach
27	chr15:78317800-78326600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:78317800-78326600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:78317800-78326600	Weak transcription	Spleen	Spleen
30	chr15:78317800-78331000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:78317800-78344400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:78317800-78344400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:78318400-78325800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr15:78318400-78326800	Weak transcription	HepG2	liver
35	chr15:78318800-78326600	Weak transcription	Stomach Mucosa	stomach
36	chr15:78319600-78326600	Weak transcription	Colonic Mucosa	Colon
37	chr15:78320000-78325800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:78320000-78326000	Weak transcription	HUVEC	blood vessel
39	chr15:78320200-78327600	Weak transcription	Fetal Brain Female	brain
40	chr15:78320200-78334400	Weak transcription	Aorta	Aorta
41	chr15:78320400-78326200	Weak transcription	Brain Substantia Nigra	brain
42	chr15:78320400-78326600	Weak transcription	Pancreas	Pancrea
43	chr15:78320400-78326800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:78320400-78331800	Weak transcription	Esophagus	oesophagus
45	chr15:78320600-78326600	Weak transcription	Left Ventricle	heart
46	chr15:78321000-78326600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:78321000-78326800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:78321200-78326600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:78321200-78343800	Weak transcription	NHEK	skin
50	chr15:78321400-78326600	Weak transcription	Stomach Smooth Muscle	stomach

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