Variant report

Variant	rs71458814
Chromosome Location	chr12:124196891-124196892
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr12:124196541-124197061	K562	blood:	n/a	n/a
2	EBF1	chr12:124196560-124197269	GM12878	blood:	n/a	n/a
3	NFIC	chr12:124196355-124197101	ECC-1	luminal epithelium:	n/a	n/a
4	RUNX3	chr12:124196401-124197338	GM12878	blood:	n/a	n/a
5	ELF1	chr12:124196553-124197013	HepG2	liver:	n/a	n/a
6	SIN3AK20	chr12:124196453-124197459	PANC-1	pancreas:	n/a	n/a
7	BHLHE40	chr12:124196614-124197109	GM12878	blood:	n/a	chr12:124196748-124196764 chr12:124197023-124197039
8	ELK1	chr12:124196625-124197091	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:124196152-124197267	HepG2	liver:	n/a	n/a
10	PAX5	chr12:124196580-124197052	GM12878	blood:	n/a	chr12:124197008-124197017
11	POLR2A	chr12:124196491-124197482	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:124196465-124197085	HL-60	blood:	n/a	n/a
13	CBX3	chr12:124196465-124196914	K562	blood:	n/a	n/a
14	TAF1	chr12:124196545-124197378	K562	blood:	n/a	n/a
15	TCF12	chr12:124196558-124197104	GM12878	blood:	n/a	chr12:124196754-124196761
16	GABPA	chr12:124196562-124197317	HepG2	liver:	n/a	n/a
17	E2F4	chr12:124196471-124197040	MCF10A-Er-Src	breast:	n/a	n/a
18	IRF1	chr12:124196541-124197084	K562	blood:	n/a	n/a
19	ZBTB7A	chr12:124196603-124197416	K562	blood:	n/a	n/a
20	YY1	chr12:124196849-124197175	HepG2	liver:	n/a	chr12:124197070-124197079 chr12:124197065-124197079
21	MTA3	chr12:124196294-124197131	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:124196213-124197457	MCF-7	breast:	n/a	n/a
23	POLR2A	chr12:124196231-124198295	Raji	blood:	n/a	n/a
24	POLR2A	chr12:124196482-124197480	K562	blood:	n/a	n/a
25	STAT1	chr12:124196579-124196954	GM12878	blood:	n/a	n/a
26	EGR1	chr12:124196583-124197064	H1-hESC	embryonic stem cell:	n/a	chr12:124196861-124196875
27	GABPA	chr12:124196626-124197050	H1-hESC	embryonic stem cell:	n/a	n/a
28	IRF1	chr12:124196537-124197271	K562	blood:	n/a	n/a
29	PAX5	chr12:124196787-124196952	GM12891	blood:	n/a	n/a
30	GABPA	chr12:124196443-124197549	K562	blood:	n/a	n/a
31	TEAD4	chr12:124196462-124197210	K562	blood:	n/a	n/a
32	ELF1	chr12:124196571-124197129	HepG2	liver:	n/a	chr12:124197070-124197079
33	BCLAF1	chr12:124196473-124197401	GM12878	blood:	n/a	chr12:124197069-124197078 chr12:124196710-124196723 chr12:124196989-124197002 chr12:124197299-124197312
34	MYC	chr12:124196293-124197601	A549	lung:	n/a	chr12:124197137-124197147
35	HEY1	chr12:124196039-124197170	HepG2	liver:	n/a	chr12:124196989-124197004
36	POLR2A	chr12:124196437-124197359	GM12891	blood:	n/a	n/a
37	FOXA2	chr12:124196516-124197147	A549	lung:	n/a	n/a
38	JUND	chr12:124196804-124197101	H1-hESC	embryonic stem cell:	n/a	n/a
39	BCLAF1	chr12:124196504-124197316	GM12878	blood:	n/a	chr12:124197069-124197078 chr12:124196710-124196723 chr12:124196989-124197002 chr12:124197299-124197312
40	CHD1	chr12:124196641-124197336	GM12878	blood:	n/a	n/a
41	MXI1	chr12:124196447-124197573	GM12878	blood:	n/a	n/a
42	GABPA	chr12:124196478-124197065	A549	lung:	n/a	n/a
43	MAZ	chr12:124196580-124197405	GM12878	blood:	n/a	n/a
44	TBP	chr12:124196499-124197079	GM12878	blood:	n/a	n/a
45	YY1	chr12:124196635-124197085	HCT-116	colon:	n/a	chr12:124197070-124197079 chr12:124197065-124197079
46	ETS1	chr12:124196515-124197285	K562	blood:	n/a	chr12:124197243-124197256 chr12:124196719-124196728
47	POLR2A	chr12:124196251-124197445	PFSK-1	brain:	n/a	n/a
48	ETS1	chr12:124196625-124197086	K562	blood:	n/a	chr12:124196719-124196728
49	POLR2A	chr12:124196501-124197190	K562	blood:	n/a	n/a
50	POLR2A	chr12:124196427-124199209	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123847805..123850449-chr12:124195534..124198038,2	K562	blood:
2	chr12:124118119..124120182-chr12:124196891..124198426,2	K562	blood:
3	chr12:124196655..124197422-chr7:107220206..107220978,2	Hela-S3	cervix:
4	chr12:124116424..124121252-chr12:124194298..124198817,7	K562	blood:
5	chr12:124196776..124197549-chr19:531664..532196,2	HCT-116	colon:
6	chr12:124196411..124197132-chr17:48450211..48450807,2	HCT-116	colon:
7	chr12:124191295..124193347-chr12:124194777..124198625,4	MCF-7	breast:
8	chr12:124141910..124144216-chr12:124195360..124197441,2	MCF-7	breast:
9	chr12:124155376..124157580-chr12:124194948..124197481,2	K562	blood:
10	chr12:124195456..124198460-chr12:124455550..124458339,3	MCF-7	breast:
11	chr12:124195458..124197705-chr12:124223204..124225071,2	MCF-7	breast:
12	chr12:124115420..124119615-chr12:124195159..124199573,8	MCF-7	breast:
13	chr12:124195749..124198082-chr12:124236149..124239807,3	MCF-7	breast:
14	chr12:124155436..124158746-chr12:124195101..124198299,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255839	TF binding region
ATP6V0A2	TF binding region
ENSG00000108826	Chromatin interaction
ENSG00000168778	Chromatin interaction
ENSG00000255839	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000185344	Chromatin interaction
ENSG00000099804	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000154920	Chromatin interaction
ENSG00000272854	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000075790	Chromatin interaction
ENSG00000179195	Chromatin interaction
ENSG00000119242	Chromatin interaction
ENSG00000178882	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1051793	0.86[EUR][1000 genomes]
rs1060637	0.81[EUR][1000 genomes]
rs1060639	0.81[EUR][1000 genomes]
rs10846537	0.83[EUR][1000 genomes]
rs1139320	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11572920	0.81[EUR][1000 genomes]
rs11572952	0.83[EUR][1000 genomes]
rs11609591	0.89[EUR][1000 genomes]
rs11610473	0.84[EUR][1000 genomes]
rs11611354	0.93[EUR][1000 genomes]
rs11611450	0.91[EUR][1000 genomes]
rs11612030	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11612479	0.93[EUR][1000 genomes]
rs11612927	0.83[EUR][1000 genomes]
rs11613632	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11614155	0.93[EUR][1000 genomes]
rs11614468	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11614659	0.90[EUR][1000 genomes]
rs11615162	0.83[EUR][1000 genomes]
rs11829958	0.89[EUR][1000 genomes]
rs11830462	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11831536	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11833604	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11834141	0.91[EUR][1000 genomes]
rs11834492	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11834808	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12811354	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12813758	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12817576	0.83[EUR][1000 genomes]
rs12817757	0.93[EUR][1000 genomes]
rs12818596	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12819746	0.90[EUR][1000 genomes]
rs12820195	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12821242	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12822546	0.94[EUR][1000 genomes]
rs12823866	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12824075	0.94[EUR][1000 genomes]
rs12825800	0.90[EUR][1000 genomes]
rs12827074	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12828408	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12828633	0.89[EUR][1000 genomes]
rs12829893	0.93[EUR][1000 genomes]
rs12829984	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12830927	0.81[EUR][1000 genomes]
rs12831081	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1515815	0.81[EUR][1000 genomes]
rs1962020	0.89[EUR][1000 genomes]
rs2203500	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2222060	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34534928	0.94[EUR][1000 genomes]
rs35114195	0.89[EUR][1000 genomes]
rs35158437	0.89[EUR][1000 genomes]
rs35416308	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35649708	0.87[EUR][1000 genomes]
rs35804181	0.94[EUR][1000 genomes]
rs35900897	0.89[EUR][1000 genomes]
rs35911711	0.87[EUR][1000 genomes]
rs35946281	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36018806	0.81[EUR][1000 genomes]
rs3817309	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4930708	0.86[EUR][1000 genomes]
rs6488888	0.90[EUR][1000 genomes]
rs6488891	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6488892	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6488893	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6488894	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6488897	0.90[EUR][1000 genomes]
rs66471742	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66647364	0.90[EUR][1000 genomes]
rs66690784	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67178535	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67516712	0.83[EUR][1000 genomes]
rs7133199	0.86[EUR][1000 genomes]
rs7133543	0.94[EUR][1000 genomes]
rs7133734	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7134074	0.89[EUR][1000 genomes]
rs7135267	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7135660	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7136939	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7138503	0.89[EUR][1000 genomes]
rs7294984	0.90[EUR][1000 genomes]
rs7296804	0.92[EUR][1000 genomes]
rs7297576	0.89[EUR][1000 genomes]
rs7298440	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7298831	0.89[EUR][1000 genomes]
rs7301065	0.84[EUR][1000 genomes]
rs7302649	0.94[EUR][1000 genomes]
rs7302788	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7304052	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7304837	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7305838	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7306549	0.89[EUR][1000 genomes]
rs7307008	0.94[EUR][1000 genomes]
rs7307343	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7308234	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7308862	0.89[EUR][1000 genomes]
rs7309528	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7310918	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7313032	0.89[EUR][1000 genomes]
rs7313140	0.89[EUR][1000 genomes]
rs7313261	0.89[EUR][1000 genomes]
rs73219037	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7397160	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7397230	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7397930	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7398152	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7398298	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7399224	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7953596	0.94[EUR][1000 genomes]
rs7953599	0.94[EUR][1000 genomes]
rs7958693	0.89[EUR][1000 genomes]
rs7959553	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7960951	0.88[EUR][1000 genomes]
rs7963498	0.94[EUR][1000 genomes]
rs7963968	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7964443	0.89[EUR][1000 genomes]
rs7968029	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7969130	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7969234	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7969964	0.94[EUR][1000 genomes]
rs7973155	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7973695	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7974279	0.89[EUR][1000 genomes]
rs7975119	0.94[EUR][1000 genomes]
rs7975233	0.94[EUR][1000 genomes]
rs7978447	0.94[EUR][1000 genomes]
rs7979528	0.86[AMR][1000 genomes];0.94[EUR][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
rs71458814	TCTN2	cis	Skin Sun Exposed Lower leg	GTEx
rs71458814	TCTN2	cis	Artery Tibial	GTEx
rs71458814	ATP6V0A2	cis	Nerve Tibial	GTEx
rs71458814	TCTN2	cis	lung	GTEx
rs71458814	TCTN2	cis	Thyroid	GTEx
rs71458814	TCTN2	cis	Muscle Skeletal	GTEx
rs71458814	TCTN2	cis	Esophagus Muscularis	GTEx
rs71458814	TCTN2	cis	Adipose Subcutaneous	GTEx
rs71458814	TCTN2	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124195800-124197600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:124195800-124197600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:124195800-124197800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr12:124195800-124197800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr12:124195800-124197800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:124196000-124197000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:124196000-124197000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:124196000-124197400	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr12:124196000-124197600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:124196000-124197600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:124196000-124197600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:124196000-124197600	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr12:124196000-124197600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr12:124196000-124197600	Active TSS	Brain Cingulate Gyrus	brain
15	chr12:124196000-124197600	Active TSS	Colon Smooth Muscle	Colon
16	chr12:124196000-124197600	Active TSS	Left Ventricle	heart
17	chr12:124196000-124197600	Active TSS	Rectal Smooth Muscle	rectum
18	chr12:124196000-124197600	Active TSS	Right Ventricle	heart
19	chr12:124196000-124197600	Active TSS	Thymus	Thymus
20	chr12:124196000-124197600	Active TSS	A549	lung
21	chr12:124196000-124197600	Active TSS	Osteobl	bone
22	chr12:124196000-124197800	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr12:124196000-124197800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr12:124196000-124197800	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr12:124196000-124197800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:124196000-124197800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:124196000-124197800	Active TSS	Brain Anterior Caudate	brain
28	chr12:124196000-124197800	Active TSS	Fetal Kidney	kidney
29	chr12:124196000-124197800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr12:124196000-124197800	Active TSS	Ovary	ovary
31	chr12:124196000-124198000	Active TSS	H9 Cell Line	embryonic stem cell
32	chr12:124196000-124198000	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:124196000-124198000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:124196000-124198000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:124196000-124198200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:124196000-124198200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:124196000-124198400	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr12:124196000-124198400	Active TSS	Psoas Muscle	Psoas
39	chr12:124196200-124197000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:124196200-124197000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:124196200-124197400	Active TSS	Primary T cells from cord blood	blood
42	chr12:124196200-124197400	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr12:124196200-124197600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr12:124196200-124197600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:124196200-124197600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:124196200-124197600	Active TSS	Brain Angular Gyrus	brain
47	chr12:124196200-124197600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:124196200-124197600	Active TSS	Esophagus	oesophagus
49	chr12:124196200-124197600	Active TSS	Fetal Heart	heart
50	chr12:124196200-124197600	Active TSS	Stomach Mucosa	stomach

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