Variant report

Variant	rs6672802
Chromosome Location	chr1:239551891-239551892
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10733125	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1938229	1.00[AMR][1000 genomes]
rs7511888	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7556590	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1006640	chr1:239290853-239658788	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535358	chr1:239290853-239658788	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv468617	chr1:239350728-239564682	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv549434	chr1:239350728-239564682	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1002418	chr1:239355675-239552376	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1001152	chr1:239355675-239564682	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1013763	chr1:239356155-239564682	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv869803	chr1:239360129-239566743	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats 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
11	nsv873349	chr1:239475925-239587512	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3373454	chr1:239495349-239670615	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv873350	chr1:239498915-239648140	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv833037	chr1:239522168-239699412	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239548800-239552400	Active TSS	Ovary	ovary
2	chr1:239548800-239553200	Active TSS	Stomach Smooth Muscle	stomach
3	chr1:239549200-239552200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:239549200-239552200	Bivalent/Poised TSS	Fetal Kidney	kidney
5	chr1:239549200-239552200	Active TSS	Pancreas	Pancrea
6	chr1:239549200-239552400	Active TSS	Colon Smooth Muscle	Colon
7	chr1:239549200-239552800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:239549400-239552000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:239549600-239552000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
10	chr1:239549600-239552200	Bivalent/Poised TSS	Fetal Brain Female	brain
11	chr1:239550000-239552400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
12	chr1:239550600-239552000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
13	chr1:239550800-239552000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
14	chr1:239551200-239552000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
15	chr1:239551200-239552400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:239551600-239552000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr1:239551600-239552000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:239551600-239552200	Bivalent Enhancer	Fetal Lung	lung
19	chr1:239551600-239552200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr1:239551600-239552400	Active TSS	Brain Anterior Caudate	brain
21	chr1:239551600-239552400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:239551600-239552400	Active TSS	Fetal Stomach	stomach
23	chr1:239551600-239552400	Active TSS	Rectal Smooth Muscle	rectum
24	chr1:239551600-239552600	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr1:239551600-239553400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:239551600-239554600	Weak transcription	Lung	lung
27	chr1:239551800-239552000	Flanking Bivalent TSS/Enh	Fetal Heart	heart
28	chr1:239551800-239552200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
29	chr1:239551800-239552200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
30	chr1:239551800-239552200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
31	chr1:239551800-239552400	Active TSS	Primary hematopoietic stem cells	blood
32	chr1:239551800-239552400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr1:239551800-239552400	Active TSS	Fetal Intestine Small	intestine

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