Variant report

Variant	rs13023980
Chromosome Location	chr2:98502987-98502988
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	chr2:98501614..98503209-chr2:98521833..98524518,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10432626	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11678558	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs11678591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11679828	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11680018	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11680321	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11680883	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11681535	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11684749	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11686881	0.91[CEU][hapmap]
rs11687510	0.87[CEU][hapmap]
rs11688829	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11690687	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11690737	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11691494	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11692010	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11692470	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12052222	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12052836	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12052846	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12104810	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12988571	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12995673	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13004090	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13006932	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13008968	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13020776	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13028954	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13032265	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13032883	0.84[EUR][1000 genomes]
rs13033383	0.91[CEU][hapmap]
rs13034929	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1470483	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17488834	0.92[CEU][hapmap]
rs17488897	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17489454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17489915	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17489984	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17490429	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1838797	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2044458	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2044459	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2084176	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2278700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305143	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2871183	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3192177	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs3198055	0.81[EUR][1000 genomes]
rs34149969	0.81[EUR][1000 genomes]
rs34373359	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34502870	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34503448	0.83[EUR][1000 genomes]
rs34528940	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34654057	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34974566	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35098301	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35218942	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35255677	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35424768	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35505530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35564270	0.82[EUR][1000 genomes]
rs35783535	0.84[EUR][1000 genomes]
rs4311104	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55776387	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55886305	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57681139	0.92[ASN][1000 genomes]
rs58546246	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62156511	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6710088	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6711101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6738389	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6746768	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6748124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6757357	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71412824	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71429376	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs717417	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7421146	0.91[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7564773	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7583868	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7601898	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895438	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs953320	1.00[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr2:98500800-98504000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:98500800-98505000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:98500800-98505000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:98500800-98505400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:98501000-98503200	ZNF genes & repeats	Brain Hippocampus Middle	brain
6	chr2:98501000-98503400	ZNF genes & repeats	Fetal Brain Male	brain
7	chr2:98501000-98503600	ZNF genes & repeats	Fetal Kidney	kidney
8	chr2:98501000-98503800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
9	chr2:98501000-98503800	ZNF genes & repeats	HSMM	muscle
10	chr2:98501000-98504000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:98501000-98504000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:98501000-98504000	ZNF genes & repeats	Primary B cells from cord blood	blood
13	chr2:98501000-98504000	ZNF genes & repeats	Fetal Brain Female	brain
14	chr2:98501000-98504600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:98501200-98503200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:98501200-98503600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
17	chr2:98501200-98504000	ZNF genes & repeats	Fetal Intestine Large	intestine
18	chr2:98501200-98505200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr2:98501400-98503000	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:98501400-98503400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:98501400-98504000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr2:98501600-98504000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:98501600-98504000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr2:98501600-98504000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
25	chr2:98501600-98504200	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr2:98501600-98504800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:98502000-98503000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:98502000-98503000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
29	chr2:98502000-98503000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:98502000-98503200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:98502000-98503200	ZNF genes & repeats	Adipose Nuclei	Adipose
32	chr2:98502000-98503400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:98502000-98503400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:98502000-98503800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
35	chr2:98502000-98503800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
36	chr2:98502000-98503800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
37	chr2:98502000-98503800	ZNF genes & repeats	HSMMtube	muscle
38	chr2:98502000-98503800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
39	chr2:98502000-98504000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr2:98502000-98504200	ZNF genes & repeats	Brain Germinal Matrix	brain
41	chr2:98502000-98504400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:98502000-98504600	ZNF genes & repeats	Dnd41	blood
43	chr2:98502000-98505000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:98502200-98503200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr2:98502200-98503200	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
46	chr2:98502200-98503400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
47	chr2:98502200-98503400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
48	chr2:98502200-98503400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
49	chr2:98502200-98503400	ZNF genes & repeats	HepG2	liver
50	chr2:98502200-98503600	ZNF genes & repeats	Primary T cells from cord blood	blood

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