Variant report

Variant	rs72942898
Chromosome Location	chr2:98530266-98530267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr2:98530205-98530746	SK-N-SH	brain:	n/a	n/a
2	ZNF143	chr2:98530195-98530321	GM12878	blood:	n/a	n/a
3	GATA2	chr2:98530263-98530747	SH-SY5Y	brain:	n/a	chr2:98530505-98530521 chr2:98530505-98530521 chr2:98530502-98530523
4	EBF1	chr2:98530163-98530477	GM12878	blood:	n/a	chr2:98530345-98530354 chr2:98530344-98530354 chr2:98530343-98530354 chr2:98530345-98530354 chr2:98530343-98530356
5	EBF1	chr2:98530130-98530502	GM12878	blood:	n/a	chr2:98530345-98530354 chr2:98530344-98530354 chr2:98530343-98530354 chr2:98530345-98530354 chr2:98530343-98530356
6	NFIC	chr2:98530068-98530575	GM12878	blood:	n/a	n/a
7	WRNIP1	chr2:98530212-98530438	GM12878	blood:	n/a	n/a
8	GATA3	chr2:98530137-98530900	SK-N-SH	brain:	n/a	chr2:98530505-98530521 chr2:98530505-98530521 chr2:98530502-98530523
9	EP300	chr2:98530079-98530881	SK-N-SH	brain:	n/a	chr2:98530147-98530161
10	TCF12	chr2:98530165-98530851	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr2:98530210-98530856	SK-N-SH	brain:	n/a	chr2:98530505-98530521 chr2:98530505-98530521 chr2:98530502-98530523
12	EBF1	chr2:98530136-98531658	GM12878	blood:	n/a	chr2:98530345-98530354 chr2:98530344-98530354 chr2:98530343-98530354 chr2:98530345-98530354 chr2:98530343-98530356
13	RUNX3	chr2:98530125-98530700	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98525688..98528111-chr2:98529878..98532703,2	MCF-7	breast:

Variant related genes	Relation type
RNU7-96P	TF binding region

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

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11892146	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895466	1.00[AMR][1000 genomes]
rs11898394	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900781	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900903	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11903844	0.94[AFR][1000 genomes]
rs1503201	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503203	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022209	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022289	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022557	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022726	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022736	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17025339	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2309318	0.85[AFR][1000 genomes]
rs35774346	0.89[AFR][1000 genomes]
rs56065241	1.00[AMR][1000 genomes]
rs57434542	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58187838	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60828800	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60885334	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61712471	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6543226	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726775	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734701	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6736475	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6737992	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742955	0.94[AFR][1000 genomes]
rs6746457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942824	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942830	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942834	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942836	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942856	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942862	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942871	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942872	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942876	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942882	0.89[AFR][1000 genomes]
rs72942885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942894	0.94[AFR][1000 genomes]
rs72942896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944812	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944813	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944818	0.81[AFR][1000 genomes]
rs72944825	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944834	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944842	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946409	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946410	0.85[AFR][1000 genomes]
rs72946417	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946421	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946425	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946431	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946447	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946448	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946453	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7579764	0.88[AFR][1000 genomes];1.00[AMR][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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98503800-98536400	Weak transcription	HSMMtube	muscle
2	chr2:98504000-98533800	Weak transcription	Spleen	Spleen
3	chr2:98504000-98538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:98504000-98540600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:98504000-98540800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:98504200-98530800	Weak transcription	Thymus	Thymus
7	chr2:98504600-98540800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:98504600-98552200	Weak transcription	NHLF	lung
9	chr2:98507600-98535000	Weak transcription	Brain Anterior Caudate	brain
10	chr2:98509000-98536400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:98515800-98540800	Weak transcription	Aorta	Aorta
12	chr2:98516400-98534600	Weak transcription	A549	lung
13	chr2:98519600-98541600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:98519800-98538600	Weak transcription	Gastric	stomach
15	chr2:98520200-98546000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:98520200-98552200	Weak transcription	Brain Angular Gyrus	brain
17	chr2:98520600-98550600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:98520800-98540400	Weak transcription	Lung	lung
19	chr2:98521200-98532800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:98521800-98540400	Weak transcription	Colonic Mucosa	Colon
21	chr2:98523200-98536200	Weak transcription	Ovary	ovary
22	chr2:98523200-98540600	Weak transcription	Right Ventricle	heart
23	chr2:98523400-98536000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:98523400-98536400	Weak transcription	Esophagus	oesophagus
25	chr2:98523400-98536600	Weak transcription	HSMM	muscle
26	chr2:98523400-98540600	Weak transcription	Fetal Brain Female	brain
27	chr2:98523400-98545800	Weak transcription	Fetal Kidney	kidney
28	chr2:98523400-98546200	Weak transcription	HUVEC	blood vessel
29	chr2:98523600-98530800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:98523800-98537600	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:98524400-98532600	Weak transcription	HMEC	breast
32	chr2:98524600-98552600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:98524800-98530400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:98524800-98532400	Enhancers	Primary B cells from peripheral blood	blood
35	chr2:98524800-98532400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:98524800-98540800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:98524800-98552200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:98525000-98530600	Weak transcription	Dnd41	blood
39	chr2:98525000-98532400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:98525000-98534000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:98525000-98536000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:98525000-98536200	Weak transcription	Placenta	Placenta
43	chr2:98525000-98538600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:98525000-98539200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:98525000-98540600	Weak transcription	Adipose Nuclei	Adipose
46	chr2:98525000-98551600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:98525200-98532600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:98525200-98538800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:98525200-98547400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:98525600-98531800	Weak transcription	Fetal Muscle Leg	muscle

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