Variant report

Variant	rs13008678
Chromosome Location	chr2:98503305-98503306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10167772	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10168543	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10168709	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169155	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10175129	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10176826	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10180434	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10180837	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10183768	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10184393	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10184457	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10184552	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10188497	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10188713	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10189414	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10192322	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10206684	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10208070	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10210299	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10210880	0.83[EUR][1000 genomes]
rs11893437	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11894541	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11895170	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11897301	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12712117	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12712147	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12712162	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12712163	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12712172	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12992955	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13000585	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13008904	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13009300	0.91[ASN][1000 genomes]
rs13012645	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387725	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13404788	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13427422	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1446327	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1503202	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1960329	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1982336	0.81[EUR][1000 genomes]
rs2293679	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305142	0.82[EUR][1000 genomes]
rs34305873	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35185431	0.81[EUR][1000 genomes]
rs35203092	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35402416	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776557	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35807655	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35940587	0.84[EUR][1000 genomes]
rs36079497	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3821053	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55817781	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707719	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707750	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712078	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6713504	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6718982	0.83[EUR][1000 genomes]
rs6721323	0.80[EUR][1000 genomes]
rs6721467	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6751727	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6756969	0.83[EUR][1000 genomes]
rs718159	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7557495	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7578638	0.83[EUR][1000 genomes]
rs7588227	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7591374	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7594928	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7595039	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7599043	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7605288	0.84[EUR][1000 genomes]
rs9784011	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9808558	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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:121 , 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	chr2:98501000-98503400	ZNF genes & repeats	Fetal Brain Male	brain
6	chr2:98501000-98503600	ZNF genes & repeats	Fetal Kidney	kidney
7	chr2:98501000-98503800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
8	chr2:98501000-98503800	ZNF genes & repeats	HSMM	muscle
9	chr2:98501000-98504000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:98501000-98504000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:98501000-98504000	ZNF genes & repeats	Primary B cells from cord blood	blood
12	chr2:98501000-98504000	ZNF genes & repeats	Fetal Brain Female	brain
13	chr2:98501000-98504600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:98501200-98503600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
15	chr2:98501200-98504000	ZNF genes & repeats	Fetal Intestine Large	intestine
16	chr2:98501200-98505200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
17	chr2:98501400-98503400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:98501400-98504000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr2:98501600-98504000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:98501600-98504000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr2:98501600-98504000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr2:98501600-98504200	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr2:98501600-98504800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:98502000-98503400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:98502000-98503400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:98502000-98503800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
27	chr2:98502000-98503800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
28	chr2:98502000-98503800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
29	chr2:98502000-98503800	ZNF genes & repeats	HSMMtube	muscle
30	chr2:98502000-98503800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
31	chr2:98502000-98504000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr2:98502000-98504200	ZNF genes & repeats	Brain Germinal Matrix	brain
33	chr2:98502000-98504400	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:98502000-98504600	ZNF genes & repeats	Dnd41	blood
35	chr2:98502000-98505000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:98502200-98503400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
37	chr2:98502200-98503400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
38	chr2:98502200-98503400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
39	chr2:98502200-98503400	ZNF genes & repeats	HepG2	liver
40	chr2:98502200-98503600	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr2:98502200-98503800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
42	chr2:98502200-98503800	ZNF genes & repeats	Liver	Liver
43	chr2:98502200-98503800	ZNF genes & repeats	Brain Substantia Nigra	brain
44	chr2:98502200-98504000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
45	chr2:98502200-98504000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr2:98502200-98504000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:98502200-98504000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:98502200-98504000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:98502200-98504200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:98502400-98503400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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