Variant report

Variant	rs2235390
Chromosome Location	chr6:11770512-11770513
allele	A/C
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	E2F6	chr6:11770469-11770658	K562	blood:	n/a	n/a
2	RCOR1	chr6:11770125-11771435	K562	blood:	n/a	n/a
3	POLR2A	chr6:11770447-11772220	Hela-S3	cervix:	n/a	n/a
4	MAZ	chr6:11770509-11771647	Hela-S3	cervix:	n/a	chr6:11771581-11771590 chr6:11771225-11771241
5	POLR2A	chr6:11769556-11773164	MCF10A-Er-Src	breast:	n/a	n/a
6	MAX	chr6:11770476-11771486	K562	blood:	n/a	chr6:11771225-11771241
7	TBP	chr6:11770213-11772070	Hela-S3	cervix:	n/a	n/a
8	MAX	chr6:11770434-11772198	Hela-S3	cervix:	n/a	chr6:11771581-11771590 chr6:11771225-11771241
9	SMC3	chr6:11770477-11772096	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr6:11768296-11772928	HUVEC	blood vessel:	n/a	n/a
11	ZBTB7A	chr6:11770345-11770654	K562	blood:	n/a	n/a
12	CTCF	chr6:11770460-11770610	NHEK	skin:	n/a	n/a
13	MAZ	chr6:11770476-11771492	K562	blood:	n/a	chr6:11771225-11771241
14	POLR2A	chr6:11770369-11772178	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr6:11770029-11772460	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr6:11770149-11770721	HUVEC	blood vessel:	n/a	n/a
17	MYC	chr6:11770484-11771558	MCF10A-Er-Src	breast:	n/a	chr6:11771225-11771241
18	BHLHE40	chr6:11770436-11770700	K562	blood:	n/a	n/a
19	MYC	chr6:11770451-11771334	K562	blood:	n/a	chr6:11771225-11771241
20	MAX	chr6:11770350-11770748	K562	blood:	n/a	n/a
21	SMARCB1	chr6:11770385-11772139	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr6:11770476-11772210	Hela-S3	cervix:	n/a	n/a
23	MAZ	chr6:11770186-11772100	IMR90	lung:	n/a	chr6:11771581-11771590 chr6:11771225-11771241
24	CEBPB	chr6:11770500-11772203	Hela-S3	cervix:	n/a	n/a
25	GTF2F1	chr6:11770478-11772134	Hela-S3	cervix:	n/a	n/a
26	FOS	chr6:11770506-11771531	MCF10A-Er-Src	breast:	n/a	n/a
27	TBL1XR1	chr6:11770151-11770706	K562	blood:	n/a	n/a
28	NR2F2	chr6:11770353-11771236	K562	blood:	n/a	n/a
29	POLR2A	chr6:11770128-11773065	IMR90	lung:	n/a	n/a
30	USF2	chr6:11770421-11770657	Hela-S3	cervix:	n/a	n/a
31	JUND	chr6:11770237-11770712	K562	blood:	n/a	n/a
32	POLR2A	chr6:11770428-11771805	Hela-S3	cervix:	n/a	n/a
33	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
34	FOS	chr6:11770485-11770582	MCF10A-Er-Src	breast:	n/a	n/a
35	CHD2	chr6:11770402-11772024	Hela-S3	cervix:	n/a	n/a
36	SMARCC2	chr6:11770482-11771791	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr6:11769228-11773136	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:11766846..11771135-chr6:12008831..12011747,3	K562	blood:
2	chr6:11755867..11758010-chr6:11770135..11772213,2	K562	blood:
3	chr6:11770371..11771301-chr7:35840308..35841252,2	Hela-S3	cervix:
4	chr6:11765488..11768224-chr6:11770343..11774117,3	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: 1 )

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

rs_ID	r²[population]
rs2235392	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2294421	0.81[EUR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2235390	C6orf105	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11760600-11770600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:11762600-11770600	Weak transcription	Spleen	Spleen
3	chr6:11763200-11773400	Enhancers	HUVEC	blood vessel
4	chr6:11764400-11770600	Weak transcription	Esophagus	oesophagus
5	chr6:11764400-11770600	Weak transcription	Left Ventricle	heart
6	chr6:11764400-11770600	Weak transcription	Right Atrium	heart
7	chr6:11765000-11770600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:11765800-11770600	Enhancers	HSMM	muscle
9	chr6:11765800-11770600	Enhancers	Osteobl	bone
10	chr6:11765800-11773000	Enhancers	NH-A	brain
11	chr6:11765800-11773600	Enhancers	NHDF-Ad	bronchial
12	chr6:11765800-11773600	Enhancers	NHLF	lung
13	chr6:11766000-11770800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:11766200-11770800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:11766600-11770800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:11766800-11770600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr6:11766800-11771800	Enhancers	Fetal Intestine Small	intestine
18	chr6:11766800-11773000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:11767000-11771800	Enhancers	Stomach Mucosa	stomach
20	chr6:11767200-11770600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:11767200-11770800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:11767400-11770600	Weak transcription	Fetal Lung	lung
23	chr6:11767600-11771000	Enhancers	HSMMtube	muscle
24	chr6:11767600-11771200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:11767800-11770800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:11768000-11770600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:11768400-11770800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:11768400-11771000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:11768400-11772000	Enhancers	Fetal Intestine Large	intestine
30	chr6:11768600-11770600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr6:11768600-11771400	Weak transcription	Aorta	Aorta
32	chr6:11768600-11774200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:11768800-11770600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:11769000-11772600	Enhancers	Small Intestine	intestine
35	chr6:11769200-11770600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr6:11769200-11770800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:11769200-11770800	Weak transcription	Psoas Muscle	Psoas
38	chr6:11769200-11771000	Flanking Active TSS	NHEK	skin
39	chr6:11769200-11771800	Enhancers	Fetal Thymus	thymus
40	chr6:11769200-11771800	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr6:11769400-11774000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:11769600-11771000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr6:11769600-11773800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr6:11769800-11770600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:11769800-11770600	Weak transcription	Gastric	stomach
46	chr6:11769800-11770800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:11769800-11770800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:11769800-11771800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:11770000-11770600	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr6:11770000-11771200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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