Variant report

Variant	rs4886998
Chromosome Location	chr15:78354276-78354277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78346803..78349725-chr15:78352567..78355144,4	MCF-7	breast:
2	chr15:78354121..78356578-chr15:78356635..78358699,2	K562	blood:
3	chr15:78347166..78349130-chr15:78354163..78355850,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167202	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1053506	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10775214	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10775215	1.00[ASN][1000 genomes]
rs11072725	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072726	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11633329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633569	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636889	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]
rs11854102	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12595595	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898535	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.81[AMR][1000 genomes];1.00[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12915847	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916320	1.00[ASN][1000 genomes]
rs1348256	1.00[CEU][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]
rs16969502	1.00[CEU][hapmap]
rs17477813	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
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];0.88[AMR][1000 genomes];1.00[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];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044100	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867984	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680277	1.00[ASN][1000 genomes]
rs3972617	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243072	1.00[ASN][1000 genomes]
rs4243073	0.86[AFR][1000 genomes]
rs4316722	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4377127	1.00[CEU][hapmap]
rs4411474	1.00[ASN][1000 genomes]
rs4886551	1.00[ASN][1000 genomes]
rs4886552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886556	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886990	1.00[ASN][1000 genomes]
rs4886991	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]
rs4886993	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]
rs4886997	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887001	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887002	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887003	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4887004	1.00[ASN][1000 genomes]
rs4997420	0.82[AFR][1000 genomes]
rs61732053	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163997	1.00[ASN][1000 genomes]
rs7169381	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7169882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170101	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170286	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]
rs7170452	1.00[CEU][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]
rs7174640	1.00[CEU][hapmap]
rs7175192	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175235	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175975	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027530	1.00[CEU][hapmap]
rs8033216	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]
rs894295	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]
rs894296	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.83[AMR][1000 genomes];1.00[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];0.86[AMR][1000 genomes];1.00[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];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:123 , 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	chr15:78344800-78357600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr15:78344800-78359800	Weak transcription	Fetal Brain Female	brain
4	chr15:78346400-78356600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:78346800-78354400	Enhancers	Primary B cells from cord blood	blood
6	chr15:78347000-78357400	Enhancers	Fetal Thymus	thymus
7	chr15:78347400-78367800	Enhancers	Placenta	Placenta
8	chr15:78348000-78355400	Enhancers	Primary B cells from peripheral blood	blood
9	chr15:78349400-78357400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:78349400-78360800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:78350200-78354600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr15:78351200-78354400	Enhancers	Spleen	Spleen
13	chr15:78352000-78357000	Weak transcription	HMEC	breast
14	chr15:78352000-78357400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:78352200-78354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:78352200-78356000	Weak transcription	Gastric	stomach
17	chr15:78352200-78356200	Weak transcription	Colonic Mucosa	Colon
18	chr15:78352200-78356200	Weak transcription	Esophagus	oesophagus
19	chr15:78352800-78354400	Weak transcription	Pancreas	Pancrea
20	chr15:78352800-78357600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:78353000-78355400	Enhancers	Left Ventricle	heart
22	chr15:78353200-78354400	Weak transcription	Lung	lung
23	chr15:78353800-78356200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:78354000-78354800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:78354000-78354800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:78354000-78354800	Flanking Active TSS	NHDF-Ad	bronchial
27	chr15:78354000-78355000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:78354000-78355000	Active TSS	GM12878-XiMat	blood
29	chr15:78354200-78354400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:78354200-78354400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:78354200-78354400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:78354200-78354400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:78354200-78354400	Enhancers	Fetal Intestine Small	intestine
34	chr15:78354200-78354400	Flanking Active TSS	Fetal Kidney	kidney
35	chr15:78354200-78354400	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr15:78354200-78354400	Flanking Active TSS	Psoas Muscle	Psoas
37	chr15:78354200-78354400	Active TSS	Right Atrium	heart
38	chr15:78354200-78354400	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr15:78354200-78354400	Flanking Active TSS	K562	blood
40	chr15:78354200-78354600	Enhancers	H1 Cell Line	embryonic stem cell
41	chr15:78354200-78354600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:78354200-78354600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:78354200-78354600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr15:78354200-78354600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:78354200-78354600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:78354200-78354600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:78354200-78354600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr15:78354200-78354600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr15:78354200-78354600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:78354200-78354600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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