Variant report

Variant	rs12997838
Chromosome Location	chr2:149284931-149284932
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:149282589..149285549-chr2:149375360..149378026,2	MCF-7	breast:
2	chr2:149281731..149283651-chr2:149284269..149286431,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10928399	0.83[AMR][1000 genomes]
rs10928404	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10928407	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12464036	0.86[EUR][1000 genomes]
rs12468186	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12472738	0.92[EUR][1000 genomes]
rs12616115	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12997473	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13003132	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13008203	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13010027	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13029692	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16828791	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16828816	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16828836	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16828954	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16828967	0.92[EUR][1000 genomes]
rs16829034	0.92[EUR][1000 genomes]
rs1809051	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2382231	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34324924	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34671855	0.86[EUR][1000 genomes]
rs34881950	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35057193	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35076661	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35154707	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35168772	0.92[EUR][1000 genomes]
rs36067597	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4972369	0.87[ASN][1000 genomes]
rs4972375	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6430323	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6709767	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6746352	0.92[EUR][1000 genomes]
rs6756002	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71413623	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7578059	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7597133	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7599758	0.82[ASN][1000 genomes]
rs7606475	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs764386	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs930651	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs930652	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012275	chr2:149031668-149316793	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2751831	chr2:149151358-150105603	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1000101	chr2:149165813-149361220	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv868861	chr2:149198443-149434604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv917109	chr2:149198443-149948302	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv1004663	chr2:149214090-149373061	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2762913	chr2:149249683-149345487	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv527539	chr2:149283070-149330251	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149247600-149291000	Weak transcription	Spleen	Spleen
2	chr2:149267000-149286200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:149267200-149285400	Weak transcription	GM12878-XiMat	blood
4	chr2:149267200-149285600	Weak transcription	HSMMtube	muscle
5	chr2:149267400-149285200	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:149267400-149288400	Weak transcription	Fetal Brain Female	brain
7	chr2:149267400-149288800	Weak transcription	Right Ventricle	heart
8	chr2:149267600-149285200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:149270600-149288400	Weak transcription	Fetal Heart	heart
10	chr2:149272400-149288800	Weak transcription	Left Ventricle	heart
11	chr2:149272600-149287600	Weak transcription	Pancreas	Pancrea
12	chr2:149273000-149286600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:149277200-149287000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:149278200-149285000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:149278800-149285200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:149280200-149287200	Enhancers	Thymus	Thymus
17	chr2:149281000-149288000	Enhancers	Fetal Thymus	thymus
18	chr2:149281400-149292200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:149281400-149296400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:149282600-149285000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:149282600-149285200	Weak transcription	Dnd41	blood
22	chr2:149282800-149285000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:149283000-149288800	Weak transcription	Right Atrium	heart
24	chr2:149283400-149285200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:149283800-149287200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr2:149284000-149286800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr2:149284200-149286600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr2:149284400-149285600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:149284400-149285600	Enhancers	Primary hematopoietic stem cells	blood
30	chr2:149284400-149286400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:149284400-149290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:149284600-149285000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr2:149284600-149285000	Enhancers	Lung	lung
34	chr2:149284600-149285400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:149284600-149286400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:149284800-149285000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:149284800-149285200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:149284800-149285800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:149284800-149285800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:149284800-149285800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr2:149284800-149286200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:149284800-149286400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:149284800-149286400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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