Variant report

Variant	rs28498454
Chromosome Location	chr4:152996669-152996670
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152994631..152998650-chr4:152999260..153001615,3	K562	blood:
2	chr4:152994994..152996876-chr4:152998778..153001469,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10013642	0.93[AFR][1000 genomes]
rs10032354	0.88[AFR][1000 genomes]
rs11940799	0.83[AFR][1000 genomes]
rs17028529	1.00[EUR][1000 genomes]
rs17028536	1.00[EUR][1000 genomes]
rs17028537	1.00[EUR][1000 genomes]
rs17028543	1.00[EUR][1000 genomes]
rs2051	0.90[AFR][1000 genomes]
rs28562808	0.95[AFR][1000 genomes]
rs28573237	0.93[AFR][1000 genomes]
rs28585419	0.93[AFR][1000 genomes]
rs28634294	0.93[AFR][1000 genomes]
rs28640127	0.90[AFR][1000 genomes]
rs28681446	0.95[AFR][1000 genomes]
rs56178482	1.00[EUR][1000 genomes]
rs57279473	0.98[EUR][1000 genomes]
rs58364558	1.00[EUR][1000 genomes]
rs61396838	1.00[EUR][1000 genomes]
rs66776773	1.00[EUR][1000 genomes]
rs67298257	1.00[EUR][1000 genomes]
rs67947413	1.00[EUR][1000 genomes]
rs72734212	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734214	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734217	1.00[EUR][1000 genomes]
rs72734218	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734219	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734220	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734221	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734223	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734226	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734228	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72734229	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72734235	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72953023	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152983800-153000800	Enhancers	Fetal Thymus	thymus
2	chr4:152985200-153000000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:152986800-152998000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:152989400-153000400	Enhancers	Thymus	Thymus
5	chr4:152990400-152997600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:152990400-152998600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:152990400-153000000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:152993000-152996800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:152994600-152998800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:152995000-152997600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr4:152995400-152996800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr4:152995400-153000600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:152995400-153000800	Enhancers	Primary T cells from cord blood	blood
14	chr4:152995800-152996800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr4:152995800-152997000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:152996000-152996800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:152996000-152996800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:152996000-152997000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr4:152996000-153000000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:152996200-152996800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr4:152996200-152997400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:152996200-152998400	Enhancers	Dnd41	blood
23	chr4:152996400-152996800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr4:152996400-152997000	Enhancers	H9 Cell Line	embryonic stem cell
25	chr4:152996600-152996800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:152996600-152997200	Enhancers	Fetal Heart	heart
27	chr4:152996600-153002800	Enhancers	Primary T helper cells fromperipheralblood	blood

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