Variant report

Variant	rs772921
Chromosome Location	chr12:56403577-56403578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr12:56402729-56404778	K562	blood:	n/a	chr12:56404260-56404273 chr12:56404389-56404400

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56398217..56408038-chr12:56433794..56439966,15	K562	blood:
2	chr12:56224367..56226323-chr12:56401356..56403743,2	MCF-7	breast:
3	chr12:56221600..56223437-chr12:56403520..56406122,2	MCF-7	breast:
4	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
5	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
6	chr12:56399898..56405642-chr12:56433175..56438589,7	K562	blood:
7	chr12:56390809..56392348-chr12:56401235..56403925,2	K562	blood:
8	chr12:56400079..56406275-chr12:56406695..56413732,8	MCF-7	breast:
9	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:

No data

Variant related genes	Relation type
IKZF4	TF binding region
ENSG00000139531	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000135392	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10876864	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10876866	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10876870	0.94[JPT][hapmap]
rs11171739	0.94[JPT][hapmap]
rs1131017	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1689510	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1701704	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1702877	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1873914	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2017445	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2048036	0.82[EUR][1000 genomes]
rs2069408	0.84[CHB][hapmap]
rs2271194	0.94[JPT][hapmap]
rs2292239	0.86[CEU][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap]
rs2456973	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2640562	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2640564	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34415530	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3741499	0.86[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs4759229	0.86[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs61937247	0.82[EUR][1000 genomes]
rs61937248	0.82[EUR][1000 genomes]
rs61937249	0.82[EUR][1000 genomes]
rs61938962	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61938963	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs705698	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs705699	0.89[CHB][hapmap]
rs705700	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs705702	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs705704	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs705705	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7302200	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs772920	0.84[EUR][1000 genomes]
rs773107	0.86[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs773108	0.90[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs773109	0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs773110	0.82[EUR][1000 genomes]
rs773111	0.82[EUR][1000 genomes]
rs773112	0.82[EUR][1000 genomes]
rs773114	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7971751	0.94[JPT][hapmap]
rs877636	0.86[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs772921	RAB5B	cis	Muscle Skeletal	GTEx
rs772921	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs772921	DEFB124	trans	lymphoblastoid	RTeQTL
rs772921	MYL6B	cis	cerebellum	SCAN
rs772921	SUOX	cis	parietal	SCAN
rs772921	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL
rs772921	KRT82	cis	parietal	SCAN
rs772921	RPS26	cis	multi-tissue	Pritchard
rs772921	AC034102.1	cis	Muscle Skeletal	GTEx
rs772921	SUOX	cis	cerebellum	SCAN
rs772921	SUOX	cis	Thyroid	GTEx
rs772921	DNAJC14	cis	parietal	SCAN
rs772921	SMARCC2	cis	parietal	SCAN
rs772921	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs772921	RPS26	cis	lymphoblastoid	seeQTL
rs772921	CSRNP2	cis	parietal	SCAN
rs772921	TAC3	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56402000-56418600	Weak transcription	Gastric	stomach
2	chr12:56402200-56403600	Weak transcription	Small Intestine	intestine
3	chr12:56402200-56404200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:56402200-56404400	Enhancers	Adipose Nuclei	Adipose
5	chr12:56402200-56404600	Enhancers	Fetal Intestine Small	intestine
6	chr12:56402200-56404800	Enhancers	K562	blood
7	chr12:56402200-56405200	Weak transcription	Aorta	Aorta
8	chr12:56402200-56405400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:56402200-56405400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr12:56402200-56405400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:56402200-56405400	Weak transcription	HSMM	muscle
12	chr12:56402200-56407200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:56402200-56407400	Weak transcription	Colonic Mucosa	Colon
14	chr12:56402200-56408200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:56402200-56409200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:56402200-56411200	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:56402200-56411800	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:56402200-56412600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:56402200-56413200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:56402200-56413400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:56402200-56413800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:56402200-56413800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:56402200-56414000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:56402200-56414000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:56402200-56414200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:56402200-56414200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:56402200-56414400	Weak transcription	Primary B cells from cord blood	blood
28	chr12:56402200-56414400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:56402200-56414400	Weak transcription	Brain Angular Gyrus	brain
30	chr12:56402200-56414400	Weak transcription	Brain Substantia Nigra	brain
31	chr12:56402200-56414400	Weak transcription	Left Ventricle	heart
32	chr12:56402200-56414400	Weak transcription	Right Ventricle	heart
33	chr12:56402200-56414400	Weak transcription	Spleen	Spleen
34	chr12:56402200-56414600	Weak transcription	Thymus	Thymus
35	chr12:56402200-56415000	Weak transcription	Lung	lung
36	chr12:56402200-56415200	Weak transcription	NH-A	brain
37	chr12:56402200-56418400	Weak transcription	Pancreas	Pancrea
38	chr12:56402200-56418400	Weak transcription	HSMMtube	muscle
39	chr12:56402200-56434800	Weak transcription	Psoas Muscle	Psoas
40	chr12:56402400-56404200	Weak transcription	Fetal Lung	lung
41	chr12:56402400-56404400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:56402400-56404400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:56402400-56404400	Enhancers	Fetal Kidney	kidney
44	chr12:56402400-56405200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:56402400-56405200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr12:56402400-56405400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:56402400-56405400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:56402400-56405400	Weak transcription	Hela-S3	cervix
49	chr12:56402400-56407400	Weak transcription	Fetal Brain Female	brain
50	chr12:56402400-56407400	Weak transcription	Stomach Mucosa	stomach

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