Variant report

Variant	rs742224
Chromosome Location	chr6:11770814-11770815
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	RFX5	chr6:11770547-11772075	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr6:11770125-11771435	K562	blood:	n/a	n/a
3	SMARCC1	chr6:11770563-11772476	Hela-S3	cervix:	n/a	n/a
4	E2F6	chr6:11770780-11771702	A549	lung:	n/a	n/a
5	RAD21	chr6:11770588-11772074	Hela-S3	cervix:	n/a	chr6:11771659-11771673
6	SP1	chr6:11770760-11771818	HCT-116	colon:	n/a	chr6:11770864-11770873 chr6:11770863-11770873 chr6:11771014-11771028
7	POLR2A	chr6:11770447-11772220	Hela-S3	cervix:	n/a	n/a
8	MAZ	chr6:11770509-11771647	Hela-S3	cervix:	n/a	chr6:11771581-11771590 chr6:11771225-11771241
9	POLR2A	chr6:11769556-11773164	MCF10A-Er-Src	breast:	n/a	n/a
10	MAX	chr6:11770476-11771486	K562	blood:	n/a	chr6:11771225-11771241
11	TBP	chr6:11770213-11772070	Hela-S3	cervix:	n/a	n/a
12	MYC	chr6:11770729-11771613	MCF10A-Er-Src	breast:	n/a	chr6:11771581-11771590 chr6:11771225-11771241
13	MAX	chr6:11770434-11772198	Hela-S3	cervix:	n/a	chr6:11771581-11771590 chr6:11771225-11771241
14	TCF7L2	chr6:11770526-11771751	Hela-S3	cervix:	n/a	n/a
15	SMC3	chr6:11770477-11772096	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:11768296-11772928	HUVEC	blood vessel:	n/a	n/a
17	MAZ	chr6:11770476-11771492	K562	blood:	n/a	chr6:11771225-11771241
18	POLR2A	chr6:11770369-11772178	Hela-S3	cervix:	n/a	n/a
19	BRCA1	chr6:11770592-11771487	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr6:11770029-11772460	HUVEC	blood vessel:	n/a	n/a
21	RUNX3	chr6:11770793-11771262	GM12878	blood:	n/a	n/a
22	FOS	chr6:11770762-11772159	MCF10A-Er-Src	breast:	n/a	n/a
23	MYC	chr6:11770484-11771558	MCF10A-Er-Src	breast:	n/a	chr6:11771225-11771241
24	EP300	chr6:11770811-11771762	SK-N-SH	brain:	n/a	n/a
25	TFAP2C	chr6:11770551-11771818	Hela-S3	cervix:	n/a	n/a
26	EP300	chr6:11770759-11771524	Hela-S3	cervix:	n/a	n/a
27	MYC	chr6:11770451-11771334	K562	blood:	n/a	chr6:11771225-11771241
28	STAT3	chr6:11770597-11772157	MCF10A-Er-Src	breast:	n/a	chr6:11771621-11771632 chr6:11770740-11770752 chr6:11771012-11771024 chr6:11771047-11771058 chr6:11771304-11771316
29	SMARCB1	chr6:11770385-11772139	Hela-S3	cervix:	n/a	n/a
30	STAT3	chr6:11770595-11772064	MCF10A-Er-Src	breast:	n/a	chr6:11771621-11771632 chr6:11770740-11770752 chr6:11771012-11771024 chr6:11771047-11771058 chr6:11771304-11771316
31	FOS	chr6:11770813-11772156	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr6:11770476-11772210	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr6:11770541-11772059	Hela-S3	cervix:	n/a	n/a
34	MAZ	chr6:11770186-11772100	IMR90	lung:	n/a	chr6:11771581-11771590 chr6:11771225-11771241
35	POLR2A	chr6:11770786-11771697	HUVEC	blood vessel:	n/a	n/a
36	MTA3	chr6:11770728-11771295	GM12878	blood:	n/a	n/a
37	CEBPB	chr6:11770500-11772203	Hela-S3	cervix:	n/a	n/a
38	GTF2F1	chr6:11770478-11772134	Hela-S3	cervix:	n/a	n/a
39	FOS	chr6:11770506-11771531	MCF10A-Er-Src	breast:	n/a	n/a
40	NR2F2	chr6:11770353-11771236	K562	blood:	n/a	n/a
41	POLR2A	chr6:11770128-11773065	IMR90	lung:	n/a	n/a
42	ZKSCAN1	chr6:11770523-11772103	Hela-S3	cervix:	n/a	n/a
43	ELK1	chr6:11770540-11771420	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr6:11770428-11771805	Hela-S3	cervix:	n/a	n/a
45	EGR1	chr6:11770797-11771611	HCT-116	colon:	n/a	chr6:11771210-11771223
46	SP1	chr6:11770727-11771809	HCT-116	colon:	n/a	chr6:11770864-11770873 chr6:11770863-11770873 chr6:11771014-11771028
47	MAX	chr6:11770778-11771813	A549	lung:	n/a	chr6:11771581-11771590 chr6:11771225-11771241
48	STAT3	chr6:11770500-11772071	MCF10A-Er-Src	breast:	n/a	chr6:11771621-11771632 chr6:11770740-11770752 chr6:11771012-11771024 chr6:11771047-11771058 chr6:11771304-11771316
49	MAFK	chr6:11770685-11771513	Hela-S3	cervix:	n/a	n/a
50	KAP1	chr6:11770552-11771527	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:11766846..11771135-chr6:12008831..12011747,3	K562	blood:
2	chr6:11760325..11763713-chr6:11770760..11773174,3	MCF-7	breast:
3	chr6:11755867..11758010-chr6:11770135..11772213,2	K562	blood:
4	chr6:11770371..11771301-chr7:35840308..35841252,2	Hela-S3	cervix:
5	chr6:11765488..11768224-chr6:11770343..11774117,3	MCF-7	breast:
6	chr6:11770626..11772377-chr6:11773316..11774913,2	MCF-7	breast:

Variant related genes	Relation type
ADTRP	TF binding region
ENSG00000111863	Chromatin interaction
ENSG00000095951	Chromatin interaction
ENSG00000122545	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs742225	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760787	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv522039	chr6:11769280-11771259	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs742224	TBC1D7	cis	parietal	SCAN
rs742224	ERVFRDE1	cis	parietal	SCAN
rs742224	C6orf105	cis	lymphoblastoid	seeQTL
rs742224	C6orf105	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11763200-11773400	Enhancers	HUVEC	blood vessel
2	chr6:11765800-11773000	Enhancers	NH-A	brain
3	chr6:11765800-11773600	Enhancers	NHDF-Ad	bronchial
4	chr6:11765800-11773600	Enhancers	NHLF	lung
5	chr6:11766800-11771800	Enhancers	Fetal Intestine Small	intestine
6	chr6:11766800-11773000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:11767000-11771800	Enhancers	Stomach Mucosa	stomach
8	chr6:11767600-11771000	Enhancers	HSMMtube	muscle
9	chr6:11767600-11771200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:11768400-11771000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:11768400-11772000	Enhancers	Fetal Intestine Large	intestine
12	chr6:11768600-11771400	Weak transcription	Aorta	Aorta
13	chr6:11768600-11774200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:11769000-11772600	Enhancers	Small Intestine	intestine
15	chr6:11769200-11771000	Flanking Active TSS	NHEK	skin
16	chr6:11769200-11771800	Enhancers	Fetal Thymus	thymus
17	chr6:11769200-11771800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr6:11769400-11774000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:11769600-11771000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr6:11769600-11773800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:11769800-11771800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:11770000-11771200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr6:11770000-11771200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr6:11770000-11771200	Enhancers	Fetal Muscle Leg	muscle
25	chr6:11770000-11771200	Flanking Active TSS	HMEC	breast
26	chr6:11770000-11771400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:11770000-11773200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr6:11770000-11773600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:11770200-11771400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr6:11770200-11771600	Enhancers	GM12878-XiMat	blood
31	chr6:11770200-11771800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:11770200-11771800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:11770200-11771800	Enhancers	Lung	lung
34	chr6:11770200-11772000	Enhancers	Colon Smooth Muscle	Colon
35	chr6:11770200-11772000	Flanking Active TSS	Hela-S3	cervix
36	chr6:11770200-11773200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr6:11770400-11771000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:11770400-11771000	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr6:11770400-11771000	Enhancers	Fetal Muscle Trunk	muscle
40	chr6:11770400-11771400	Enhancers	Fetal Stomach	stomach
41	chr6:11770400-11771400	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr6:11770400-11771400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr6:11770400-11771600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr6:11770400-11771800	Enhancers	Placenta	Placenta
45	chr6:11770400-11772200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:11770400-11772600	Enhancers	H9 Cell Line	embryonic stem cell
47	chr6:11770600-11771000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:11770600-11771000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:11770600-11771000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:11770600-11771000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links