Variant report

Variant	rs17023620
Chromosome Location	chr2:39522731-39522732
allele	A/T
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	chr2:39522696-39522769	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
MAP4K3	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10490305	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11886110	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11898704	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11902188	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17023552	1.00[JPT][hapmap]
rs17023573	0.87[ASN][1000 genomes]
rs17038958	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55961227	0.84[AFR][1000 genomes]
rs56024079	0.82[ASN][1000 genomes]
rs56850142	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56928728	0.87[AFR][1000 genomes]
rs58005382	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58824151	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59121834	0.82[ASN][1000 genomes]
rs59459399	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59707152	0.90[AFR][1000 genomes]
rs61219633	0.84[AFR][1000 genomes]
rs6544225	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6712399	0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6723987	0.82[AFR][1000 genomes]
rs6725784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6727395	1.00[CHB][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6751506	1.00[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73923842	0.87[ASN][1000 genomes]
rs73923844	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73923848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73923887	0.84[AFR][1000 genomes]
rs73923888	0.84[AFR][1000 genomes]
rs73923889	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73923895	0.85[AFR][1000 genomes]
rs7591563	0.81[AFR][1000 genomes]
rs7599017	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
19	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
20	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
21	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
22	esv1828851	chr2:39508121-39588797	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv873888	chr2:39508830-39573521	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39476600-39527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39478600-39543400	Weak transcription	Stomach Mucosa	stomach
3	chr2:39481000-39580200	Weak transcription	NHEK	skin
4	chr2:39493600-39523800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:39493600-39565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:39493800-39525000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:39494000-39525600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:39494000-39553000	Weak transcription	GM12878-XiMat	blood
9	chr2:39495600-39523200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:39504600-39523600	Weak transcription	Brain Substantia Nigra	brain
11	chr2:39504600-39540000	Weak transcription	Right Ventricle	heart
12	chr2:39504600-39562000	Weak transcription	Psoas Muscle	Psoas
13	chr2:39504800-39527800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:39504800-39538400	Weak transcription	Small Intestine	intestine
15	chr2:39504800-39541600	Weak transcription	Fetal Brain Male	brain
16	chr2:39504800-39565800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:39504800-39567200	Weak transcription	Hela-S3	cervix
18	chr2:39505000-39523400	Weak transcription	Brain Germinal Matrix	brain
19	chr2:39505000-39527400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:39505000-39538200	Weak transcription	Lung	lung
21	chr2:39505400-39556800	Weak transcription	Thymus	Thymus
22	chr2:39505400-39557200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:39505400-39562400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:39505600-39540000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:39507200-39538400	Weak transcription	Aorta	Aorta
26	chr2:39508800-39527400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:39510200-39524000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:39513600-39523400	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:39513600-39555000	Weak transcription	Primary B cells from cord blood	blood
30	chr2:39514400-39539800	Weak transcription	A549	lung
31	chr2:39514400-39541800	Weak transcription	HUVEC	blood vessel
32	chr2:39515200-39538600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:39516200-39557600	Weak transcription	Gastric	stomach
34	chr2:39517200-39552400	Weak transcription	HMEC	breast
35	chr2:39517600-39566400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:39519000-39523600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:39519000-39531600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr2:39519000-39531800	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:39519000-39538600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:39519000-39555200	Weak transcription	Fetal Thymus	thymus
41	chr2:39519800-39523000	Weak transcription	Spleen	Spleen
42	chr2:39519800-39526600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:39519800-39527400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:39519800-39527800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:39519800-39538400	Weak transcription	Brain Anterior Caudate	brain
46	chr2:39519800-39538400	Weak transcription	Esophagus	oesophagus
47	chr2:39519800-39553000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr2:39519800-39555400	Weak transcription	Fetal Heart	heart
49	chr2:39519800-39562200	Weak transcription	K562	blood
50	chr2:39519800-39583000	Weak transcription	Brain Angular Gyrus	brain

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