Variant report

Variant	rs12077340
Chromosome Location	chr1:59034199-59034200
allele	A/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	USF1	chr1:59034138-59034610	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr1:59034138-59034635	ECC-1	luminal epithelium:	n/a	chr1:59034346-59034357 chr1:59034348-59034357 chr1:59034345-59034358 chr1:59034345-59034360 chr1:59034349-59034356 chr1:59034347-59034357 chr1:59034347-59034356 chr1:59034347-59034357 chr1:59034345-59034358
3	TCF12	chr1:59034007-59034650	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:59011936..59013636-chr1:59031728..59034428,2	K562	blood:
2	chr1:59027310..59029958-chr1:59032688..59035404,2	MCF-7	breast:
3	chr1:59032420..59036590-chr1:59038071..59040162,4	K562	blood:
4	chr1:59034065..59036590-chr1:59038071..59040103,2	K562	blood:
5	chr1:59033300..59036238-chr1:59156402..59159118,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL713P	TF binding region
ENSG00000162600	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10458559	0.88[ASN][1000 genomes]
rs10789064	0.88[ASN][1000 genomes]
rs10789065	0.85[ASN][1000 genomes]
rs10789066	0.88[ASN][1000 genomes]
rs10889099	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10889100	0.88[ASN][1000 genomes]
rs10889101	0.88[ASN][1000 genomes]
rs10889104	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1109895	0.88[ASN][1000 genomes]
rs1109896	0.88[ASN][1000 genomes]
rs11207246	0.82[ASN][1000 genomes]
rs11207247	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11207248	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11207250	0.88[ASN][1000 genomes]
rs11207251	0.88[ASN][1000 genomes]
rs11207252	0.88[ASN][1000 genomes]
rs11207253	0.88[ASN][1000 genomes]
rs11207254	0.88[ASN][1000 genomes]
rs11207255	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207260	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207262	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207264	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207265	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207266	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207267	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207268	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11581594	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11582299	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11583248	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11584788	0.81[EUR][1000 genomes]
rs11589214	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589236	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590785	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12058651	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12067296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068196	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068201	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068597	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12069688	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12070503	0.82[ASN][1000 genomes]
rs12072998	0.82[ASN][1000 genomes]
rs12077766	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12080357	0.82[ASN][1000 genomes]
rs12087583	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12092564	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12097882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125391	0.88[ASN][1000 genomes]
rs12133823	0.82[ASN][1000 genomes]
rs12139475	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12141238	0.82[ASN][1000 genomes]
rs12142098	0.88[ASN][1000 genomes]
rs12406405	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568356	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17117742	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17117873	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17117877	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17372425	0.81[EUR][1000 genomes]
rs17461345	0.81[EUR][1000 genomes]
rs2087799	0.88[ASN][1000 genomes]
rs232841	0.97[ASN][1000 genomes]
rs232842	0.97[ASN][1000 genomes]
rs232844	0.97[ASN][1000 genomes]
rs232847	0.97[ASN][1000 genomes]
rs232848	1.00[ASN][1000 genomes]
rs232849	1.00[ASN][1000 genomes]
rs2406784	0.88[ASN][1000 genomes]
rs3087585	0.82[ASN][1000 genomes]
rs34023272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893156	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3893157	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41313363	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56049576	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs562166	1.00[ASN][1000 genomes]
rs584579	1.00[ASN][1000 genomes]
rs59607787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59924197	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602579	1.00[ASN][1000 genomes]
rs603031	1.00[ASN][1000 genomes]
rs60490291	0.82[ASN][1000 genomes]
rs60726128	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61779295	0.97[ASN][1000 genomes]
rs61779296	0.97[ASN][1000 genomes]
rs620342	1.00[ASN][1000 genomes]
rs627218	1.00[ASN][1000 genomes]
rs6587820	0.82[ASN][1000 genomes]
rs6663327	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6664314	0.81[EUR][1000 genomes]
rs6666138	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6666304	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6679808	0.82[ASN][1000 genomes]
rs6690139	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6704300	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67238056	0.81[EUR][1000 genomes]
rs67264345	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67443104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67538366	0.81[EUR][1000 genomes]
rs67673245	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67805407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68192782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72672216	0.82[ASN][1000 genomes]
rs7355165	0.82[ASN][1000 genomes]
rs7355166	0.82[ASN][1000 genomes]
rs7515056	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7536867	0.82[ASN][1000 genomes]
rs7546900	0.88[ASN][1000 genomes]
rs7547070	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs905567	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12077340	TACSTD2	cis	Whole Blood	GTEx
rs12077340	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59031600-59035000	Enhancers	Psoas Muscle	Psoas
2	chr1:59032200-59034400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:59032200-59034400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:59032400-59034200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:59032600-59035000	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:59033000-59034200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:59033000-59035000	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:59033400-59034600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr1:59033400-59035000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:59033400-59035000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:59033800-59035000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:59033800-59035400	Enhancers	NHEK	skin
13	chr1:59033800-59039800	Weak transcription	Placenta Amnion	Placenta Amnion

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