Variant report

Variant	rs28369939
Chromosome Location	chr2:100081981-100081982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100080735..100084657-chr2:100090928..100093443,3	K562	blood:
2	chr2:100066815..100068950-chr2:100081584..100083548,2	K562	blood:
3	chr2:100068951..100071646-chr2:100081782..100083860,2	K562	blood:
4	chr2:100079371..100082089-chr2:100106220..100108086,2	MCF-7	breast:
5	chr2:100081842..100083413-chr2:100104447..100107377,2	MCF-7	breast:
6	chr2:100072001..100074970-chr2:100080545..100083472,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10496338	1.00[AFR][1000 genomes]
rs12466624	1.00[AFR][1000 genomes]
rs12467621	1.00[AFR][1000 genomes]
rs12468845	1.00[AFR][1000 genomes]
rs1882597	1.00[AFR][1000 genomes]
rs3087401	0.94[MEX][hapmap];0.90[AMR][1000 genomes]
rs4850900	1.00[AFR][1000 genomes]
rs6718629	1.00[AFR][1000 genomes]
rs72817037	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv874700	chr2:100062163-100099989	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
2	chr2:100041600-100083400	Weak transcription	Brain Substantia Nigra	brain
3	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
4	chr2:100055400-100083200	Weak transcription	Right Ventricle	heart
5	chr2:100055800-100089000	Weak transcription	Pancreas	Pancrea
6	chr2:100055800-100092600	Weak transcription	Gastric	stomach
7	chr2:100056600-100091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:100065400-100087400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:100073400-100090000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:100074200-100084800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:100075200-100090400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:100075200-100103000	Weak transcription	Hela-S3	cervix
13	chr2:100076200-100098400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:100076200-100105000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:100076400-100084800	Weak transcription	Esophagus	oesophagus
16	chr2:100076600-100085400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:100076600-100094800	Weak transcription	Spleen	Spleen
18	chr2:100076600-100104200	Weak transcription	NHLF	lung
19	chr2:100078400-100083200	Weak transcription	Fetal Heart	heart
20	chr2:100078400-100083400	Weak transcription	Brain Anterior Caudate	brain
21	chr2:100078400-100084800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:100078600-100084000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:100078600-100084800	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:100078600-100085000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:100078600-100085200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:100078600-100085800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:100078600-100087400	Weak transcription	HMEC	breast
28	chr2:100078600-100087600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:100078600-100088600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:100078600-100088800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:100078600-100091000	Weak transcription	Aorta	Aorta
32	chr2:100078600-100091000	Weak transcription	Lung	lung
33	chr2:100078600-100092200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:100078600-100092600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:100078600-100096800	Weak transcription	NH-A	brain
36	chr2:100078800-100082800	Weak transcription	Psoas Muscle	Psoas
37	chr2:100078800-100084800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:100078800-100084800	Weak transcription	Brain Angular Gyrus	brain
39	chr2:100078800-100084800	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:100078800-100084800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:100078800-100085000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:100078800-100085000	Weak transcription	Fetal Brain Male	brain
43	chr2:100078800-100085200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:100078800-100088800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:100078800-100089000	Weak transcription	Ovary	ovary
46	chr2:100078800-100090000	Weak transcription	HUVEC	blood vessel
47	chr2:100078800-100090200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:100078800-100090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:100078800-100091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:100078800-100091400	Weak transcription	Adipose Nuclei	Adipose

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