Variant report

Variant	rs34426406
Chromosome Location	chr3:134027610-134027611
allele	C/T
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	MAX	chr3:134027234-134027719	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr3:134027521-134027720	SK-N-SH_RA	brain:	n/a	n/a
3	RAD21	chr3:134027092-134027819	HepG2	liver:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
4	TEAD4	chr3:134027103-134027888	SK-N-SH	brain:	n/a	n/a
5	SP4	chr3:134027231-134027626	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:134027141-134027689	GM12878	blood:	n/a	chr3:134027392-134027408 chr3:134027396-134027406 chr3:134027391-134027409 chr3:134027394-134027403 chr3:134027393-134027414
7	CTCF	chr3:134027171-134027612	K562	blood:	n/a	chr3:134027392-134027408 chr3:134027396-134027406 chr3:134027391-134027409 chr3:134027394-134027403 chr3:134027393-134027414
8	ATF2	chr3:134027160-134027644	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:134027068-134027688	IMR90	lung:	n/a	chr3:134027392-134027408 chr3:134027396-134027406 chr3:134027391-134027409 chr3:134027394-134027403 chr3:134027393-134027414
10	MAX	chr3:134027260-134027850	ECC-1	luminal epithelium:	n/a	n/a
11	MYBL2	chr3:134027159-134027652	HepG2	liver:	n/a	n/a
12	CHD1	chr3:134026796-134028113	IMR90	lung:	n/a	n/a
13	MAFK	chr3:134027204-134027718	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr3:134027158-134027696	HepG2	liver:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
15	SMC3	chr3:134025597-134028095	SK-N-SH	brain:	n/a	chr3:134026526-134026533 chr3:134027397-134027407 chr3:134027393-134027400 chr3:134026592-134026599 chr3:134026269-134026276 chr3:134027393-134027407
16	RAD21	chr3:134027036-134027759	MCF-7	breast:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
17	MYC	chr3:134027179-134027731	H1-hESC	embryonic stem cell:	n/a	n/a
18	GABPA	chr3:134027453-134027857	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr3:134026904-134027957	HCT-116	colon:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
20	ZNF143	chr3:134027214-134027691	H1-hESC	embryonic stem cell:	n/a	chr3:134027577-134027596
21	CTCF	chr3:134026772-134027900	SK-N-SH	brain:	n/a	chr3:134027392-134027408 chr3:134027396-134027406 chr3:134027391-134027409 chr3:134027394-134027403 chr3:134027393-134027414
22	USF2	chr3:134027024-134027754	Hela-S3	cervix:	n/a	n/a
23	SP1	chr3:134027186-134027639	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr3:134027165-134027709	H1-hESC	embryonic stem cell:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
25	GATA3	chr3:134027147-134027612	T-47D	breast:	n/a	n/a
26	CTCF	chr3:134026957-134027978	HCT-116	colon:	n/a	chr3:134027392-134027408 chr3:134027396-134027406 chr3:134027391-134027409 chr3:134027394-134027403 chr3:134027393-134027414
27	SMC3	chr3:134026934-134027750	HepG2	liver:	n/a	chr3:134027397-134027407 chr3:134027393-134027400 chr3:134027393-134027407
28	TBP	chr3:134027305-134027672	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr3:134026954-134027875	MCF-7	breast:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
30	RAD21	chr3:134027101-134027780	SK-N-SH_RA	brain:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
31	RAD21	chr3:134027174-134027624	GM12878	blood:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
32	RAD21	chr3:134027092-134027613	A549	lung:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
33	TEAD4	chr3:134027235-134027721	A549	lung:	n/a	n/a
34	ELF1	chr3:134027297-134027614	GM12878	blood:	n/a	n/a
35	BRCA1	chr3:134027223-134027615	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr3:134027350-134027621	HepG2	liver:	n/a	n/a
37	MAZ	chr3:134027254-134027669	Hela-S3	cervix:	n/a	n/a
38	EP300	chr3:134027204-134027820	A549	lung:	n/a	n/a
39	SP1	chr3:134027120-134027823	A549	lung:	n/a	n/a
40	RAD21	chr3:134026994-134027984	ECC-1	luminal epithelium:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
41	E2F6	chr3:134027201-134027852	H1-hESC	embryonic stem cell:	n/a	n/a
42	RAD21	chr3:134026918-134027895	HCT-116	colon:	n/a	chr3:134027392-134027411 chr3:134027397-134027407
43	SIN3A	chr3:134027219-134027810	H1-hESC	embryonic stem cell:	n/a	n/a
44	YY1	chr3:134027160-134027807	H1-hESC	embryonic stem cell:	n/a	chr3:134027311-134027321
45	CEBPB	chr3:134027172-134027711	H1-hESC	embryonic stem cell:	n/a	n/a
46	CHD2	chr3:134027239-134027613	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAX	chr3:134027399-134027633	K562	blood:	n/a	n/a
48	TEAD4	chr3:134027144-134027864	ECC-1	luminal epithelium:	n/a	n/a
49	TCF7L2	chr3:134027224-134027733	Hela-S3	cervix:	n/a	chr3:134027327-134027337
50	CTCF	chr3:134027100-134027658	MCF-7	breast:	n/a	chr3:134027392-134027408 chr3:134027396-134027406 chr3:134027391-134027409 chr3:134027394-134027403 chr3:134027393-134027414

No.	Distal block	Cell Line	Cell type
1	chr3:134026945..134027852-chr3:134172592..134173161,2	MCF-7	breast:
2	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
3	chr3:134026923..134027850-chr3:134198250..134199054,2	MCF-7	breast:
4	chr3:134027115..134027630-chr3:134100230..134100993,2	MCF-7	breast:
5	chr3:134027338..134027879-chr3:134166952..134167798,2	MCF-7	breast:
6	chr3:134026993..134027640-chr3:134210825..134211549,2	K562	blood:
7	chr3:134027019..134027846-chr3:134191593..134192140,2	K562	blood:
8	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
9	chr3:134026198..134027834-chr3:134167829..134169129,15	MCF-7	breast:
10	chr3:134026977..134027845-chr3:134096964..134097732,3	MCF-7	breast:
11	chr3:134026656..134027867-chr3:134192501..134193467,17	MCF-7	breast:
12	chr3:134027313..134027882-chr3:134096935..134097746,2	K562	blood:
13	chr3:134026309..134027866-chr3:134192546..134193488,7	MCF-7	breast:
14	chr3:134020415..134022058-chr3:134026557..134028767,2	MCF-7	breast:
15	chr3:134026798..134028420-chr3:134164621..134166613,2	MCF-7	breast:
16	chr3:134027446..134029898-chr3:134199577..134201556,2	MCF-7	breast:
17	chr3:134026969..134027956-chr3:134096702..134097867,13	MCF-7	breast:
18	chr3:133929711..133931992-chr3:134027528..134029983,2	MCF-7	breast:
19	chr3:134027318..134027903-chr3:134092861..134093553,2	MCF-7	breast:
20	chr3:134026968..134027634-chr3:134090071..134090721,3	MCF-7	breast:
21	chr3:134026973..134027620-chr3:134211228..134212162,3	MCF-7	breast:
22	chr3:134026947..134027640-chr3:134198061..134198841,2	MCF-7	breast:
23	chr3:134027292..134027808-chr3:134092974..134093743,2	MCF-7	breast:
24	chr3:134027278..134027877-chr3:134192552..134193439,4	K562	blood:
25	chr3:134026918..134027856-chr3:134172237..134173017,2	K562	blood:
26	chr3:134026273..134028991-chr3:134194363..134198560,4	MCF-7	breast:
27	chr3:134027069..134028938-chr3:134191393..134194235,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240006	TF binding region
ENSG00000114019	Chromatin interaction
ENSG00000260633	Chromatin interaction
ENSG00000214289	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1344687	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2270733	0.92[ASN][1000 genomes]
rs34591691	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34596580	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34688449	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34913236	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35160848	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35369871	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4131649	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4131651	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4234420	0.92[ASN][1000 genomes]
rs4270476	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4437113	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4449291	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4470481	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4504146	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4510358	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4533618	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4558731	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4574266	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682661	0.92[ASN][1000 genomes]
rs4682663	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6774600	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71331752	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7431754	0.92[ASN][1000 genomes]
rs7614238	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621320	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7641605	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7644134	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7652144	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289466	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289467	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9863226	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34426406	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs34426406	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx
rs34426406	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs34426406	RP11-375I20.6	cis	Thyroid	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134023800-134032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:134025200-134031600	Weak transcription	Ovary	ovary
3	chr3:134025600-134030800	Weak transcription	Spleen	Spleen
4	chr3:134026000-134028600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:134026000-134029200	Enhancers	HMEC	breast
6	chr3:134026200-134028400	Enhancers	NHEK	skin
7	chr3:134026400-134028800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:134026400-134029400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:134026400-134031800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:134026600-134027800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:134026800-134027800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:134026800-134027800	Flanking Active TSS	HepG2	liver
13	chr3:134026800-134028000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr3:134026800-134029400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:134026800-134030400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:134026800-134031800	Enhancers	HSMM	muscle
17	chr3:134026800-134032400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:134026800-134034800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:134027000-134027800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:134027000-134027800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
21	chr3:134027000-134027800	Enhancers	Fetal Heart	heart
22	chr3:134027000-134027800	Enhancers	Pancreas	Pancrea
23	chr3:134027000-134027800	Enhancers	HUVEC	blood vessel
24	chr3:134027000-134028800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:134027000-134030800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:134027000-134031000	Enhancers	Liver	Liver
27	chr3:134027000-134031400	Enhancers	Duodenum Mucosa	Duodenum
28	chr3:134027000-134031600	Enhancers	Colonic Mucosa	Colon
29	chr3:134027000-134031600	Enhancers	Placenta	Placenta
30	chr3:134027000-134032200	Enhancers	Fetal Muscle Leg	muscle
31	chr3:134027000-134032400	Enhancers	HSMMtube	muscle
32	chr3:134027000-134032400	Enhancers	NH-A	brain
33	chr3:134027200-134027800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:134027200-134028000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:134027200-134029400	Enhancers	Stomach Mucosa	stomach
36	chr3:134027200-134030000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:134027400-134027800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr3:134027400-134027800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:134027400-134027800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:134027400-134027800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:134027400-134027800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:134027400-134027800	Enhancers	Brain Angular Gyrus	brain
43	chr3:134027400-134027800	Enhancers	Brain Hippocampus Middle	brain
44	chr3:134027400-134027800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:134027400-134027800	Enhancers	Left Ventricle	heart
46	chr3:134027400-134027800	Enhancers	Rectal Smooth Muscle	rectum
47	chr3:134027400-134027800	Enhancers	Right Atrium	heart
48	chr3:134027400-134028000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr3:134027400-134028000	Enhancers	Fetal Stomach	stomach
50	chr3:134027400-134028000	Enhancers	Lung	lung

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