Variant report

Variant	rs6749980
Chromosome Location	chr2:39480592-39480593
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	chr2:39476438..39480963-chr2:39481034..39484561,4	K562	blood:
2	chr2:39476355..39478295-chr2:39480403..39482715,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10490306	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17023400	0.83[AMR][1000 genomes]
rs17023430	1.00[AMR][1000 genomes]
rs17023486	0.87[AFR][1000 genomes]
rs17038956	1.00[AMR][1000 genomes]
rs55978422	1.00[AMR][1000 genomes]
rs56698739	0.92[AMR][1000 genomes]
rs57183352	1.00[AMR][1000 genomes]
rs57794248	1.00[AMR][1000 genomes]
rs61526451	1.00[AMR][1000 genomes]
rs6544208	1.00[AMR][1000 genomes]
rs6544218	0.84[AFR][1000 genomes]
rs6707666	1.00[AMR][1000 genomes]
rs6725849	0.85[AFR][1000 genomes]
rs6745059	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72921009	1.00[AMR][1000 genomes]
rs72923492	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs72923494	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs72923496	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs72923498	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72927478	1.00[AMR][1000 genomes]
rs72927499	1.00[AMR][1000 genomes]
rs73924823	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7561710	1.00[AMR][1000 genomes]
rs7563852	1.00[AMR][1000 genomes]
rs7585411	0.83[AMR][1000 genomes]
rs868841	1.00[AMR][1000 genomes]
rs9679492	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
16	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv2693	chr2:39468641-39513800	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv873886	chr2:39468676-39573521	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	esv1809158	chr2:39474679-39588797	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39469200-39503800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:39469400-39504200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39471000-39503400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:39471200-39483800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:39471200-39503800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:39471200-39504200	Weak transcription	Esophagus	oesophagus
7	chr2:39471400-39503400	Weak transcription	Right Ventricle	heart
8	chr2:39472600-39504000	Weak transcription	Thymus	Thymus
9	chr2:39472800-39481000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:39472800-39492000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:39473000-39482600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:39473000-39485600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:39473000-39491000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:39473000-39492200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:39473200-39491400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:39473400-39517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:39474400-39480600	Weak transcription	NHEK	skin
18	chr2:39474600-39482400	Strong transcription	HSMM	muscle
19	chr2:39474600-39492600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:39474600-39494600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:39474600-39494600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:39474800-39492600	Weak transcription	Psoas Muscle	Psoas
23	chr2:39475000-39483000	Strong transcription	NH-A	brain
24	chr2:39475600-39493600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:39475600-39494200	Strong transcription	Placenta	Placenta
26	chr2:39475600-39494400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:39475800-39481800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:39475800-39481800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr2:39475800-39482200	Strong transcription	Adipose Nuclei	Adipose
30	chr2:39476200-39480600	Weak transcription	K562	blood
31	chr2:39476200-39483800	Weak transcription	Hela-S3	cervix
32	chr2:39476200-39502400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:39476400-39484600	Strong transcription	HepG2	liver
34	chr2:39476600-39527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:39476800-39483800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:39477000-39487800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:39477200-39481800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:39477200-39495200	Strong transcription	Liver	Liver
39	chr2:39477400-39481800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr2:39477400-39482200	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr2:39477400-39482800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:39477600-39480800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:39477600-39480800	Strong transcription	Brain Angular Gyrus	brain
44	chr2:39477600-39481000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:39477600-39481000	Strong transcription	NHLF	lung
46	chr2:39477600-39481600	Strong transcription	Primary T cells from cord blood	blood
47	chr2:39477600-39481800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:39477600-39481800	Strong transcription	Brain Anterior Caudate	brain
49	chr2:39477600-39481800	Strong transcription	Fetal Thymus	thymus
50	chr2:39477600-39481800	Strong transcription	Ovary	ovary

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