Variant report

Variant	rs56121717
Chromosome Location	chr15:51242625-51242626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51234956..51237517-chr15:51240627..51243200,3	K562	blood:
2	chr15:51242549..51245131-chr15:51257817..51260638,2	MCF-7	breast:
3	chr15:51240708..51242711-chr15:51242889..51245874,2	K562	blood:

Variant related genes	Relation type
ENSG00000259378	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs16963979	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28865017	1.00[AMR][1000 genomes]
rs55683982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55735813	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55742119	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55763666	1.00[AMR][1000 genomes]
rs55912100	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55920356	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55940433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55973448	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56010315	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56017509	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56046825	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56049414	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56056949	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56222335	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56273151	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56283133	1.00[AMR][1000 genomes]
rs56289716	1.00[AMR][1000 genomes]
rs56374503	1.00[AMR][1000 genomes]
rs56813592	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57221782	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57305511	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57499524	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57831362	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57949904	1.00[AMR][1000 genomes]
rs58651255	1.00[AMR][1000 genomes]
rs59067851	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59155793	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59364110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59681404	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59843670	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59865784	1.00[AMR][1000 genomes]
rs60037205	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60253924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60297574	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60700183	1.00[AMR][1000 genomes]
rs60775199	1.00[AMR][1000 genomes]
rs61106666	1.00[AMR][1000 genomes]
rs61698311	1.00[AMR][1000 genomes]
rs6493467	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7171301	1.00[AMR][1000 genomes]
rs7174066	1.00[AMR][1000 genomes]
rs7175547	1.00[AMR][1000 genomes]
rs74012820	1.00[AMR][1000 genomes]
rs74012821	1.00[AMR][1000 genomes]
rs74013114	1.00[AMR][1000 genomes]
rs74013115	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013125	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013127	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013128	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013130	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74013132	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74015214	1.00[AMR][1000 genomes]
rs74015215	1.00[AMR][1000 genomes]
rs74015226	1.00[AMR][1000 genomes]
rs74015228	1.00[AMR][1000 genomes]
rs74015229	1.00[AMR][1000 genomes]
rs74015230	1.00[AMR][1000 genomes]
rs74015232	1.00[AMR][1000 genomes]
rs74015235	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74015236	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv569404	chr15:51234595-51294995	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51201600-51243200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:51201600-51245000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:51201800-51242800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:51201800-51248400	Weak transcription	Colonic Mucosa	Colon
5	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:51202600-51242800	Weak transcription	Gastric	stomach
7	chr15:51202800-51243400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:51203200-51242800	Weak transcription	Lung	lung
9	chr15:51204800-51243000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:51205600-51242800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:51205800-51249000	Weak transcription	Fetal Brain Male	brain
12	chr15:51205800-51254400	Weak transcription	Fetal Heart	heart
13	chr15:51208000-51250400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:51210400-51243000	Weak transcription	Brain Angular Gyrus	brain
15	chr15:51210600-51298400	Weak transcription	Stomach Mucosa	stomach
16	chr15:51213000-51242800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:51213200-51245400	Weak transcription	Psoas Muscle	Psoas
18	chr15:51213600-51243400	Weak transcription	Pancreas	Pancrea
19	chr15:51213800-51247600	Weak transcription	Aorta	Aorta
20	chr15:51214600-51247800	Weak transcription	Esophagus	oesophagus
21	chr15:51219800-51243000	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:51220200-51243000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:51221800-51242800	Weak transcription	Brain Anterior Caudate	brain
24	chr15:51222000-51242800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:51223400-51243000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:51223400-51243000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:51231000-51242800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:51231000-51242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:51231000-51243000	Weak transcription	Brain Germinal Matrix	brain
30	chr15:51231000-51247800	Weak transcription	Spleen	Spleen
31	chr15:51231200-51242800	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:51231200-51242800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:51232400-51243200	Weak transcription	Fetal Intestine Small	intestine
34	chr15:51232400-51250400	Weak transcription	HepG2	liver
35	chr15:51232800-51242800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:51232800-51254000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:51233200-51245000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:51233800-51254200	Strong transcription	Placenta	Placenta
39	chr15:51235200-51263800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr15:51236600-51242800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr15:51237400-51242800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:51237400-51242800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:51237400-51242800	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:51237400-51243000	Weak transcription	Right Ventricle	heart
45	chr15:51237400-51245000	Weak transcription	GM12878-XiMat	blood
46	chr15:51237400-51245600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:51237400-51246000	Weak transcription	NHLF	lung
48	chr15:51237400-51247600	Weak transcription	K562	blood
49	chr15:51237400-51249600	Weak transcription	Small Intestine	intestine
50	chr15:51237600-51242800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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