Variant report

Variant	rs10734904
Chromosome Location	chr12:124204158-124204159
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:58 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:124204026-124204465	K562	blood:	n/a	n/a
2	GATA2	chr12:124203649-124204501	SH-SY5Y	brain:	n/a	n/a
3	NR2F2	chr12:124203615-124205390	K562	blood:	n/a	n/a
4	ZMIZ1	chr12:124204137-124204513	K562	blood:	n/a	n/a
5	ARID3A	chr12:124203292-124204824	K562	blood:	n/a	n/a
6	TEAD4	chr12:124204038-124204582	K562	blood:	n/a	n/a
7	CEBPD	chr12:124203977-124204604	K562	blood:	n/a	n/a
8	SP1	chr12:124204132-124204440	K562	blood:	n/a	n/a
9	GATA1	chr12:124203407-124204901	K562	blood:	n/a	n/a
10	TAF1	chr12:124204150-124204508	K562	blood:	n/a	n/a
11	CBX3	chr12:124204091-124204561	K562	blood:	n/a	n/a
12	CUX1	chr12:124204140-124204536	K562	blood:	n/a	n/a
13	HDAC2	chr12:124204074-124204444	K562	blood:	n/a	n/a
14	TEAD4	chr12:124203640-124204706	K562	blood:	n/a	n/a
15	BHLHE40	chr12:124204117-124204946	K562	blood:	n/a	n/a
16	MYC	chr12:124203857-124204594	K562	blood:	n/a	n/a
17	CCNT2	chr12:124203830-124204556	K562	blood:	n/a	n/a
18	PML	chr12:124204026-124204567	K562	blood:	n/a	n/a
19	POLR2A	chr12:124204080-124204533	K562	blood:	n/a	n/a
20	GABPA	chr12:124204145-124204418	K562	blood:	n/a	n/a
21	POLR2A	chr12:124204097-124204577	K562	blood:	n/a	n/a
22	RCOR1	chr12:124204158-124204645	K562	blood:	n/a	n/a
23	REST	chr12:124204156-124204457	K562	blood:	n/a	n/a
24	TAL1	chr12:124203722-124204521	K562	blood:	n/a	n/a
25	TBL1XR1	chr12:124203402-124204972	K562	blood:	n/a	n/a
26	CEBPD	chr12:124204008-124204499	K562	blood:	n/a	n/a
27	PML	chr12:124204057-124204544	K562	blood:	n/a	n/a
28	RAD21	chr12:124204110-124204430	SK-N-SH_RA	brain:	n/a	n/a
29	MAZ	chr12:124203734-124204538	K562	blood:	n/a	n/a
30	MAX	chr12:124204142-124204483	K562	blood:	n/a	n/a
31	EGR1	chr12:124204145-124204546	K562	blood:	n/a	n/a
32	IRF1	chr12:124203593-124205073	K562	blood:	n/a	n/a
33	CHD2	chr12:124204147-124204392	K562	blood:	n/a	n/a
34	MAX	chr12:124204078-124204584	K562	blood:	n/a	n/a
35	RCOR1	chr12:124203722-124204680	K562	blood:	n/a	n/a
36	GATA2	chr12:124203600-124204628	K562	blood:	n/a	n/a
37	ZNF384	chr12:124203687-124204814	K562	blood:	n/a	n/a
38	HMGN3	chr12:124204151-124204458	K562	blood:	n/a	n/a
39	MYC	chr12:124203735-124204567	K562	blood:	n/a	n/a
40	REST	chr12:124204157-124204389	K562	blood:	n/a	n/a
41	GATA3	chr12:124204154-124204480	SH-SY5Y	brain:	n/a	n/a
42	JUND	chr12:124203734-124205205	K562	blood:	n/a	chr12:124204845-124204852 chr12:124204843-124204852 chr12:124204842-124204854
43	TRIM28	chr12:124203738-124204589	K562	blood:	n/a	n/a
44	POLR2A	chr12:124204152-124204476	K562	blood:	n/a	n/a
45	STAT5A	chr12:124203984-124204589	K562	blood:	n/a	n/a
46	GATA2	chr12:124204093-124204497	K562	blood:	n/a	n/a
47	GATA1	chr12:124204116-124204489	K562	blood:	n/a	n/a
48	GATA3	chr12:124204094-124204558	SK-N-SH	brain:	n/a	n/a
49	CEBPB	chr12:124204125-124204511	K562	blood:	n/a	n/a
50	ZBTB7A	chr12:124204098-124204549	K562	blood:	n/a	n/a

No data

Variant related genes	Relation type
ATP6V0A2	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10160842	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10160937	0.91[EUR][1000 genomes]
rs1040156	0.97[EUR][1000 genomes]
rs10732574	0.98[EUR][1000 genomes]
rs10734903	0.89[EUR][1000 genomes]
rs10734905	0.91[EUR][1000 genomes]
rs10734906	0.91[EUR][1000 genomes]
rs10734907	0.83[EUR][1000 genomes]
rs10734908	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10744157	0.91[EUR][1000 genomes]
rs10744158	0.91[EUR][1000 genomes]
rs10744159	0.91[EUR][1000 genomes]
rs10744160	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10744161	0.90[EUR][1000 genomes]
rs10744162	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10773026	0.91[EUR][1000 genomes]
rs10773029	0.86[EUR][1000 genomes]
rs10773030	0.91[EUR][1000 genomes]
rs10773031	0.87[EUR][1000 genomes]
rs10773032	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10773033	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10773034	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10846549	0.97[EUR][1000 genomes]
rs10846550	0.97[EUR][1000 genomes]
rs10846551	0.87[EUR][1000 genomes]
rs10846553	0.84[EUR][1000 genomes]
rs1139789	0.89[EUR][1000 genomes]
rs11837144	0.91[EUR][1000 genomes]
rs12580486	0.97[EUR][1000 genomes]
rs1399961	0.91[EUR][1000 genomes]
rs1878077	0.91[EUR][1000 genomes]
rs2176152	0.87[EUR][1000 genomes]
rs2271660	0.95[EUR][1000 genomes]
rs2271661	0.97[EUR][1000 genomes]
rs2271662	0.91[EUR][1000 genomes]
rs2333834	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2333835	0.94[EUR][1000 genomes]
rs2333836	0.97[EUR][1000 genomes]
rs2333837	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2333838	0.95[EUR][1000 genomes]
rs2333839	0.98[EUR][1000 genomes]
rs2333840	0.91[EUR][1000 genomes]
rs34247974	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6488899	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6488900	0.90[EUR][1000 genomes]
rs6488901	0.80[EUR][1000 genomes]
rs6488902	0.90[EUR][1000 genomes]
rs67516712	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7132115	0.91[EUR][1000 genomes]
rs7135542	0.88[EUR][1000 genomes]
rs7295552	0.97[EUR][1000 genomes]
rs7300721	0.98[EUR][1000 genomes]
rs7300818	0.91[EUR][1000 genomes]
rs7301641	0.89[EUR][1000 genomes]
rs7302708	0.91[EUR][1000 genomes]
rs7308398	0.97[EUR][1000 genomes]
rs7311789	0.91[EUR][1000 genomes]
rs7397240	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7397745	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7397746	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7398082	0.95[EUR][1000 genomes]
rs7398384	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7398606	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7398641	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7398851	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7399128	0.97[EUR][1000 genomes]
rs7956045	0.90[EUR][1000 genomes]
rs7956751	0.91[EUR][1000 genomes]
rs7960403	0.91[EUR][1000 genomes]
rs7974331	0.91[EUR][1000 genomes]
rs7974462	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs882563	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs968203	0.91[EUR][1000 genomes]
rs9787987	0.89[EUR][1000 genomes]
rs9788204	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv832534	chr12:124157605-124234611	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10734904	TCTN2	cis	Artery Tibial	GTEx
rs10734904	TCTN2	cis	Stomach	GTEx
rs10734904	TCTN2	cis	Esophagus Muscularis	GTEx
rs10734904	TCTN2	cis	Nerve Tibial	GTEx
rs10734904	ATP6V0A2	cis	Nerve Tibial	GTEx
rs10734904	TCTN2	cis	Thyroid	GTEx
rs10734904	TCTN2	cis	Adipose Subcutaneous	GTEx
rs10734904	TCTN2	cis	lung	GTEx
rs10734904	TCTN2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124197600-124234400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:124198200-124204400	Weak transcription	Aorta	Aorta
3	chr12:124198200-124207000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:124198200-124207200	Weak transcription	Ovary	ovary
5	chr12:124198400-124204400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:124198400-124204400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:124198400-124210600	Weak transcription	NH-A	brain
8	chr12:124198600-124205000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:124198600-124205600	Weak transcription	HSMM	muscle
10	chr12:124198600-124205800	Weak transcription	HMEC	breast
11	chr12:124198600-124206800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:124198600-124207200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:124198600-124212400	Weak transcription	NHLF	lung
14	chr12:124198800-124204200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:124198800-124204200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:124198800-124204200	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:124198800-124204400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:124198800-124204400	Weak transcription	Placenta	Placenta
19	chr12:124198800-124205000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:124198800-124205800	Weak transcription	A549	lung
21	chr12:124198800-124205800	Weak transcription	Osteobl	bone
22	chr12:124198800-124210800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:124198800-124223600	Weak transcription	Right Atrium	heart
24	chr12:124199000-124204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:124199000-124204200	Weak transcription	Left Ventricle	heart
26	chr12:124199000-124204200	Weak transcription	Lung	lung
27	chr12:124199000-124204200	Weak transcription	HSMMtube	muscle
28	chr12:124199000-124204400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:124199000-124204400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:124199000-124205600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:124199000-124206000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:124199000-124206000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:124199000-124206200	Weak transcription	NHEK	skin
34	chr12:124199000-124207000	Weak transcription	Fetal Kidney	kidney
35	chr12:124199000-124207200	Weak transcription	Brain Substantia Nigra	brain
36	chr12:124199000-124207200	Weak transcription	Esophagus	oesophagus
37	chr12:124199000-124210000	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:124199000-124212400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr12:124199200-124204200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:124199200-124204200	Weak transcription	Liver	Liver
41	chr12:124199200-124204200	Weak transcription	Brain Germinal Matrix	brain
42	chr12:124199200-124204200	Weak transcription	Fetal Brain Female	brain
43	chr12:124199200-124204200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:124199200-124204200	Weak transcription	Thymus	Thymus
45	chr12:124199200-124205800	Weak transcription	Spleen	Spleen
46	chr12:124199200-124206000	Weak transcription	HepG2	liver
47	chr12:124199200-124206200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:124199200-124206400	Weak transcription	Adipose Nuclei	Adipose
49	chr12:124199200-124207200	Weak transcription	Small Intestine	intestine
50	chr12:124199200-124210000	Weak transcription	Colonic Mucosa	Colon

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