Variant report

Variant	rs12484392
Chromosome Location	chr22:29977602-29977603
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr22:29977561-29977811	A549	lung:	n/a	n/a
2	SETDB1	chr22:29977178-29977673	U2OS	brain:	n/a	n/a
3	MAX	chr22:29977498-29977768	K562	blood:	n/a	n/a
4	POLR2A	chr22:29977576-29977711	MCF-7	breast:	n/a	n/a
5	MAX	chr22:29977547-29977898	A549	lung:	n/a	n/a
6	REST	chr22:29976056-29977674	H1-neurons	neurons:	n/a	n/a
7	MXI1	chr22:29975754-29978016	SK-N-SH	brain:	n/a	chr22:29977179-29977188
8	POLR2A	chr22:29975436-29977710	HepG2	liver:	n/a	n/a
9	E2F6	chr22:29977535-29977717	K562	blood:	n/a	n/a
10	MAX	chr22:29977560-29977811	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr22:29977574-29978173	MCF-7	breast:	n/a	n/a
12	POLR2A	chr22:29976723-29977724	MCF-7	breast:	n/a	n/a
13	POLR2A	chr22:29976318-29978116	MCF-7	breast:	n/a	n/a
14	POLR2A	chr22:29976116-29977736	Raji	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29975483..29978642-chr22:29996311..30000725,6	MCF-7	breast:
2	chr22:29947295..29951735-chr22:29976015..29980297,4	K562	blood:
3	chr22:29663275..29666008-chr22:29976454..29978804,2	K562	blood:
4	chr22:29948374..29951089-chr22:29975785..29978624,4	MCF-7	breast:
5	chr22:29782601..29785697-chr22:29975164..29978533,5	MCF-7	breast:
6	chr22:29975560..29978145-chr22:29998416..30001350,4	MCF-7	breast:
7	chr22:29948193..29950224-chr22:29975940..29978547,6	MCF-7	breast:

No data

Variant related genes	Relation type
NIPSNAP1	TF binding region
ENSG00000182944	Chromatin interaction
ENSG00000100263	Chromatin interaction
ENSG00000100296	Chromatin interaction
ENSG00000186575	Chromatin interaction
ENSG00000100280	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1058642	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11090569	0.82[EUR][1000 genomes]
rs12172347	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13054618	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13055568	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13055746	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13056992	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13057041	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800538	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1807506	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2024116	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2024119	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2024121	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240638	0.82[EUR][1000 genomes]
rs2267147	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2348677	0.83[EUR][1000 genomes]
rs2348683	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2348684	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34013089	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3940296	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4470427	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67292640	0.82[EUR][1000 genomes]
rs67884471	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs715490	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7287318	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8142111	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs867088	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9608781	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608785	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9608787	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9608789	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9608790	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9608794	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9608798	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9608799	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613956	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9613957	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9613958	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613961	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613963	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613965	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613970	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613971	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613975	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613977	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613978	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613979	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613980	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9613983	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613984	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613986	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613990	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613991	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613992	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9613993	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613994	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613995	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613996	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613997	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9613998	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9613999	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9614004	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9614006	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9614011	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9614014	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9614018	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS 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	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv521852	chr22:29974831-29983138	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12484392	THOC5	cis	Adipose Subcutaneous	GTEx
rs12484392	THOC5	cis	Artery Tibial	GTEx
rs12484392	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs12484392	THOC5	cis	Thyroid	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29975800-29977800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr22:29976000-29977800	Active TSS	Primary T cells from cord blood	blood
3	chr22:29976000-29977800	Active TSS	Fetal Kidney	kidney
4	chr22:29976200-29977800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr22:29976200-29977800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr22:29976200-29978000	Active TSS	Rectal Smooth Muscle	rectum
7	chr22:29976400-29977800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr22:29976400-29977800	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr22:29976400-29977800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr22:29976400-29977800	Active TSS	Brain Anterior Caudate	brain
11	chr22:29976400-29977800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr22:29976600-29977800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr22:29976600-29977800	Active TSS	Brain Substantia Nigra	brain
14	chr22:29976600-29978000	Active TSS	A549	lung
15	chr22:29976800-29977800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:29976800-29977800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr22:29976800-29977800	Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr22:29976800-29977800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:29976800-29977800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr22:29976800-29977800	Active TSS	Adipose Nuclei	Adipose
21	chr22:29976800-29977800	Active TSS	Brain Angular Gyrus	brain
22	chr22:29976800-29977800	Active TSS	Brain Cingulate Gyrus	brain
23	chr22:29976800-29977800	Active TSS	Brain Germinal Matrix	brain
24	chr22:29976800-29977800	Active TSS	Brain Hippocampus Middle	brain
25	chr22:29976800-29977800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr22:29976800-29977800	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr22:29976800-29977800	Active TSS	Fetal Brain Female	brain
28	chr22:29976800-29977800	Active TSS	Stomach Smooth Muscle	stomach
29	chr22:29976800-29977800	Active TSS	HSMM	muscle
30	chr22:29976800-29977800	Active TSS	HUVEC	blood vessel
31	chr22:29976800-29978200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr22:29977000-29977800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr22:29977000-29977800	Active TSS	Colonic Mucosa	Colon
34	chr22:29977200-29977800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr22:29977200-29977800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr22:29977200-29977800	Active TSS	Fetal Heart	heart
37	chr22:29977200-29977800	Flanking Active TSS	Fetal Thymus	thymus
38	chr22:29977200-29978200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:29977200-29978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr22:29977400-29977800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr22:29977400-29977800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr22:29977400-29977800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr22:29977400-29977800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr22:29977400-29977800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr22:29977400-29977800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr22:29977400-29977800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr22:29977400-29977800	Enhancers	Liver	Liver
48	chr22:29977400-29977800	Enhancers	Fetal Brain Male	brain
49	chr22:29977400-29977800	Enhancers	Left Ventricle	heart
50	chr22:29977400-29977800	Enhancers	Lung	lung

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