Variant report

Variant	rs16830088
Chromosome Location	chr2:152341118-152341119
allele	A/G
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	POLR2A	chr2:152337487-152344157	K562	blood:	n/a	n/a
2	POLR2A	chr2:152340724-152341193	K562	blood:	n/a	n/a
3	POLR2A	chr2:152341095-152341137	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr2:152340721-152341793	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
RIF1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12619249	1.00[EUR][1000 genomes]
rs12623646	1.00[EUR][1000 genomes]
rs13413290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16829912	1.00[AMR][1000 genomes]
rs16830087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16830140	1.00[EUR][1000 genomes]
rs16830170	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16830173	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16830174	1.00[EUR][1000 genomes]
rs16830189	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16830216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16830236	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3213817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35967764	1.00[EUR][1000 genomes]
rs41525550	0.90[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73004051	1.00[EUR][1000 genomes]
rs73004053	1.00[EUR][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	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv834418	chr2:152205803-152385516	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv933869	chr2:152308156-152391576	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv437298	chr2:152320118-152356361	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv3693428	chr2:152320932-152434896	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152267600-152379400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:152268000-152342800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:152268600-152342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:152295800-152348400	Weak transcription	Right Ventricle	heart
5	chr2:152301800-152343800	Weak transcription	Gastric	stomach
6	chr2:152304800-152354000	Weak transcription	Spleen	Spleen
7	chr2:152314000-152344000	Weak transcription	Esophagus	oesophagus
8	chr2:152314000-152349400	Weak transcription	Pancreas	Pancrea
9	chr2:152320400-152343800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:152320800-152343600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:152320800-152358600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:152324000-152348800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:152324200-152382400	Weak transcription	Aorta	Aorta
14	chr2:152325600-152348800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:152326200-152344200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:152326200-152347400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:152326400-152367400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:152326600-152348000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:152327200-152342600	Weak transcription	Small Intestine	intestine
20	chr2:152327200-152343800	Weak transcription	Thymus	Thymus
21	chr2:152327200-152347400	Weak transcription	Brain Angular Gyrus	brain
22	chr2:152327400-152342800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:152327400-152343400	Weak transcription	Fetal Brain Male	brain
24	chr2:152327400-152344800	Weak transcription	Brain Anterior Caudate	brain
25	chr2:152327800-152342600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:152327800-152346800	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:152327800-152347800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:152328400-152344000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:152328400-152347000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:152328600-152342600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:152329400-152341600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:152329400-152342800	Strong transcription	Fetal Thymus	thymus
33	chr2:152329400-152344200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:152330600-152346800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:152331200-152342200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:152332000-152345400	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:152332000-152350400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:152332200-152344600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:152332400-152350800	Weak transcription	NHDF-Ad	bronchial
40	chr2:152333000-152342200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr2:152333400-152341800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:152333400-152343200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:152334000-152349400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:152334200-152342400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:152334400-152343400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:152334400-152343800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:152335000-152342600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr2:152335000-152346800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:152335200-152349400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr2:152336000-152341200	Strong transcription	Primary T cells fromperipheralblood	blood

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