Variant report

Variant	rs16830086
Chromosome Location	chr2:152338989-152338990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

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	chr2:152338949-152339278	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:152338983-152339139	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:152338864-152339616	HL-60	blood:	n/a	n/a
5	EBF1	chr2:152338937-152339157	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:152338781-152339422	GM12892	blood:	n/a	n/a
7	POLR2A	chr2:152338966-152339150	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:152338857-152339448	K562	blood:	n/a	n/a
9	POLR2A	chr2:152338941-152339323	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:152338932-152339216	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:152338845-152340571	A549	lung:	n/a	n/a
12	POLR2A	chr2:152338840-152339611	K562	blood:	n/a	n/a
13	POLR2A	chr2:152338874-152339965	K562	blood:	n/a	n/a
14	POLR2A	chr2:152338912-152339458	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr2:152338765-152339716	H1-hESC	embryonic stem cell:	n/a	n/a
16	RUNX3	chr2:152338243-152338990	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:152338769-152339530	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:152329635..152332984-chr2:152337072..152339089,3	K562	blood:
2	chr2:152336512..152339181-chr2:152360323..152362422,2	K562	blood:
3	chr2:152316997..152319818-chr2:152338220..152340859,2	K562	blood:
4	chr2:152333499..152335226-chr2:152337769..152339551,2	K562	blood:

No data

Variant related genes	Relation type
RIF1	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10497084	0.84[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11681877	0.82[JPT][hapmap]
rs11896481	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052998	0.83[ASN][1000 genomes]
rs16830019	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16830036	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830047	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830059	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16830061	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830067	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830090	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16830096	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16830159	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16830228	0.84[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1993206	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288206	0.85[ASN][1000 genomes]
rs2288211	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs3732308	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732312	0.81[ASN][1000 genomes]
rs4233653	0.85[JPT][hapmap]
rs4468813	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491723	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4494741	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4664057	0.82[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4664058	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4664492	0.84[ASW][hapmap]
rs55654831	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs55900984	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55982073	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56002721	0.82[ASN][1000 genomes]
rs56224718	0.84[ASN][1000 genomes]
rs56898485	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58037758	0.82[ASN][1000 genomes]
rs59723161	0.81[ASN][1000 genomes]
rs62169373	0.81[ASN][1000 genomes]
rs62169378	0.86[ASN][1000 genomes]
rs62169380	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62169382	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62169384	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169385	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62169386	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726640	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733645	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742953	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72860229	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72860230	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72860235	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72860236	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7422009	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7593710	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][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:122 , 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	chr2:152267800-152340400	Weak transcription	Stomach Mucosa	stomach
3	chr2:152268000-152342800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:152268600-152342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:152295800-152348400	Weak transcription	Right Ventricle	heart
6	chr2:152301800-152343800	Weak transcription	Gastric	stomach
7	chr2:152304800-152354000	Weak transcription	Spleen	Spleen
8	chr2:152314000-152344000	Weak transcription	Esophagus	oesophagus
9	chr2:152314000-152349400	Weak transcription	Pancreas	Pancrea
10	chr2:152320400-152339200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:152320400-152343800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:152320800-152343600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:152320800-152358600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:152321400-152340200	Weak transcription	Psoas Muscle	Psoas
15	chr2:152324000-152348800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:152324200-152382400	Weak transcription	Aorta	Aorta
17	chr2:152325600-152348800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:152326200-152344200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:152326200-152347400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:152326400-152367400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:152326600-152348000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:152327200-152339000	Weak transcription	Ovary	ovary
23	chr2:152327200-152340600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:152327200-152342600	Weak transcription	Small Intestine	intestine
25	chr2:152327200-152343800	Weak transcription	Thymus	Thymus
26	chr2:152327200-152347400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:152327400-152340000	Weak transcription	Fetal Brain Female	brain
28	chr2:152327400-152342800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:152327400-152343400	Weak transcription	Fetal Brain Male	brain
30	chr2:152327400-152344800	Weak transcription	Brain Anterior Caudate	brain
31	chr2:152327600-152339000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:152327600-152339000	Weak transcription	NHLF	lung
33	chr2:152327800-152340200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:152327800-152340200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:152327800-152340400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:152327800-152342600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:152327800-152346800	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:152327800-152347800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:152328400-152344000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:152328400-152347000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:152328600-152342600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:152329400-152341600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:152329400-152342800	Strong transcription	Fetal Thymus	thymus
44	chr2:152329400-152344200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:152329600-152340600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:152329600-152340600	Strong transcription	Dnd41	blood
47	chr2:152329600-152341000	Strong transcription	K562	blood
48	chr2:152330600-152346800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:152331200-152342200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:152331600-152340000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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