Variant report

Variant	rs6695707
Chromosome Location	chr1:160991821-160991822
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	MAFK	chr1:160991821-160992259	Hela-S3	cervix:	n/a	chr1:160991986-160992006 chr1:160991985-160992001 chr1:160991989-160992003 chr1:160991985-160992000
2	FOXA2	chr1:160991814-160992049	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:160990289-160991978	Hela-S3	cervix:	n/a	n/a
4	FOS	chr1:160991790-160992513	MCF10A-Er-Src	breast:	n/a	chr1:160991967-160991979
5	POLR2A	chr1:160989702-160991901	MCF10A-Er-Src	breast:	n/a	n/a
6	HA-E2F1	chr1:160990364-160991876	MCF-7	breast:	n/a	chr1:160990991-160991000 chr1:160991077-160991086 chr1:160991104-160991115 chr1:160991108-160991115
7	JUN	chr1:160990258-160992327	K562	blood:	n/a	chr1:160990989-160990998 chr1:160991589-160991601 chr1:160991967-160991979 chr1:160991463-160991477 chr1:160990591-160990599 chr1:160991020-160991029
8	FOSL2	chr1:160991765-160992143	A549	lung:	n/a	chr1:160991967-160991979
9	POLR2A	chr1:160990329-160991979	MCF-7	breast:	n/a	n/a
10	POLR2A	chr1:160989484-160992369	MCF10A-Er-Src	breast:	n/a	n/a
11	SMARCC1	chr1:160990308-160992327	Hela-S3	cervix:	n/a	n/a
12	FOXA1	chr1:160991716-160992201	HepG2	liver:	n/a	n/a
13	GTF2F1	chr1:160990539-160991923	Hela-S3	cervix:	n/a	n/a
14	FOSL2	chr1:160991130-160992341	A549	lung:	n/a	chr1:160991589-160991601 chr1:160991967-160991979 chr1:160991463-160991477
15	POLR2A	chr1:160990245-160992277	K562	blood:	n/a	n/a
16	FOS	chr1:160991716-160992542	MCF10A-Er-Src	breast:	n/a	chr1:160991967-160991979
17	FOXA2	chr1:160991448-160992214	A549	lung:	n/a	n/a
18	SP1	chr1:160990389-160992137	A549	lung:	n/a	chr1:160990975-160990984 chr1:160990603-160990612 chr1:160990727-160990737 chr1:160990980-160991001 chr1:160990974-160990983 chr1:160990974-160990988 chr1:160990599-160990613 chr1:160990974-160990984 chr1:160991011-160991032 chr1:160990713-160990726 chr1:160990973-160990985 chr1:160991089-160991098 chr1:160990973-160990984 chr1:160990973-160990985
19	SP1	chr1:160990520-160992114	A549	lung:	n/a	chr1:160990975-160990984 chr1:160990603-160990612 chr1:160990727-160990737 chr1:160990980-160991001 chr1:160990974-160990983 chr1:160990974-160990988 chr1:160990599-160990613 chr1:160990974-160990984 chr1:160991011-160991032 chr1:160990713-160990726 chr1:160990973-160990985 chr1:160991089-160991098 chr1:160990973-160990984 chr1:160990973-160990985
20	POLR2A	chr1:160990371-160992050	HCT-116	colon:	n/a	n/a
21	SIN3AK20	chr1:160990252-160992095	MCF-7	breast:	n/a	n/a
22	JUND	chr1:160991812-160992225	HepG2	liver:	n/a	chr1:160991967-160991979 chr1:160991972-160991983
23	ZNF263	chr1:160989702-160991978	HEK293-T-REx	kidney:	n/a	chr1:160991635-160991656 chr1:160990706-160990715 chr1:160991557-160991578
24	NFYB	chr1:160991779-160992053	Hela-S3	cervix:	n/a	n/a
25	MAX	chr1:160990284-160992375	A549	lung:	n/a	chr1:160991078-160991088 chr1:160990974-160990984
26	POLR2A	chr1:160990468-160991970	HepG2	liver:	n/a	n/a
27	MYC	chr1:160991748-160992568	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr1:160991788-160992150	MCF10A-Er-Src	breast:	n/a	chr1:160991967-160991979
29	TCF12	chr1:160990165-160992254	A549	lung:	n/a	chr1:160991067-160991074
30	FOSL2	chr1:160991768-160992133	HepG2	liver:	n/a	chr1:160991967-160991979
31	STAT3	chr1:160991811-160992466	MCF10A-Er-Src	breast:	n/a	chr1:160992106-160992117
32	NR2F2	chr1:160989320-160991875	K562	blood:	n/a	n/a
33	POLR2A	chr1:160989296-160992160	H1-hESC	embryonic stem cell:	n/a	n/a
34	CEBPB	chr1:160991813-160992305	Hela-S3	cervix:	n/a	chr1:160992052-160992063
35	RCOR1	chr1:160990636-160992332	Hela-S3	cervix:	n/a	n/a
36	FOS	chr1:160991721-160992602	MCF10A-Er-Src	breast:	n/a	chr1:160991967-160991979
37	CBX3	chr1:160990171-160991898	K562	blood:	n/a	n/a
38	POLR2A	chr1:160989724-160991933	K562	blood:	n/a	n/a
39	RCOR1	chr1:160989966-160992202	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:160989106..160992104-chr1:161101728..161103686,4	K562	blood:
2	chr1:160991163..160993549-chr1:161020053..161022442,2	MCF-7	breast:
3	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
4	chr1:160989661..160992673-chr1:161066595..161070388,4	K562	blood:
5	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:
6	chr1:160990576..160992373-chr1:161014612..161018487,6	K562	blood:
7	chr1:160989097..160992016-chr1:161278410..161280382,2	K562	blood:
8	chr1:160990813..160992339-chr17:57183553..57186254,2	MCF-7	breast:
9	chr1:160987801..160992609-chr1:161065993..161069595,4	MCF-7	breast:
10	chr1:160991301..160993466-chr1:161036693..161038459,2	K562	blood:
11	chr1:160989787..160992592-chr1:161127591..161130267,2	K562	blood:
12	chr1:160991294..160991903-chr1:161015743..161016371,2	Hela-S3	cervix:
13	chr1:160989864..160992775-chr1:161169949..161172743,2	MCF-7	breast:
14	chr1:160989663..160992818-chr1:161011844..161017868,15	MCF-7	breast:
15	chr1:160988368..160992141-chr1:161085559..161090183,5	MCF-7	breast:
16	chr1:160990492..160992160-chr1:161130814..161132595,2	K562	blood:
17	chr1:160989721..160993044-chr1:161014364..161019082,7	K562	blood:
18	chr1:160991276..160994205-chr1:161086519..161089474,3	MCF-7	breast:
19	chr1:160989661..160992673-chr1:161067559..161070388,3	K562	blood:
20	chr1:160987861..160992104-chr1:161101436..161104060,5	K562	blood:
21	chr1:160989495..160995605-chr1:161004888..161010340,15	MCF-7	breast:
22	chr1:160988819..160994033-chr1:161005548..161011188,8	MCF-7	breast:
23	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
24	chr1:160989601..160993379-chr1:161101301..161104263,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSTD1-1	chr1:160991202-160992060	NONHSAT007092

Variant related genes	Relation type
F11R	TF binding region
ENSG00000158773	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000224985	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000143258	Chromatin interaction
ENSG00000158887	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000108395	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12410477	1.00[AFR][1000 genomes]
rs1556259	0.87[TSI][hapmap]
rs1556260	0.87[TSI][hapmap]
rs16832617	0.87[TSI][hapmap]
rs2073653	0.87[TSI][hapmap]
rs4993172	0.80[CHD][hapmap]
rs57839241	0.89[EUR][1000 genomes]
rs6427573	0.87[TSI][hapmap]
rs6686076	0.87[TSI][hapmap]
rs6701822	0.86[EUR][1000 genomes]
rs7516231	0.93[TSI][hapmap]

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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6695707	SDHC	cis	parietal	SCAN
rs6695707	C1orf66	cis	parietal	SCAN
rs6695707	MNDA	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160988000-160992000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:160988600-160992000	Active TSS	H1 Cell Line	embryonic stem cell
3	chr1:160988600-160992200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:160988800-160992000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:160989000-160992000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:160989000-160992000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:160990000-160992000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:160991200-160992000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr1:160991200-160992000	Flanking Active TSS	GM12878-XiMat	blood
10	chr1:160991200-160992600	Flanking Active TSS	Hela-S3	cervix
11	chr1:160991200-160995200	Weak transcription	HSMM	muscle
12	chr1:160991200-161007800	Weak transcription	HSMMtube	muscle
13	chr1:160991400-160992000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:160991400-160992000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:160991400-160992000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:160991400-160992000	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr1:160991400-160992000	Flanking Active TSS	HepG2	liver
18	chr1:160991400-160992200	Flanking Active TSS	HMEC	breast
19	chr1:160991400-160992200	Flanking Active TSS	K562	blood
20	chr1:160991400-160992400	Flanking Active TSS	NHEK	skin
21	chr1:160991600-160992000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:160991600-160992000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:160991600-160992000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:160991600-160992000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:160991600-160992000	Enhancers	Liver	Liver
26	chr1:160991600-160992000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr1:160991600-160992000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:160991600-160992200	Enhancers	HUVEC	blood vessel
29	chr1:160991600-160992400	Flanking Active TSS	A549	lung
30	chr1:160991600-160992600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:160991600-160992800	Enhancers	Placenta	Placenta
32	chr1:160991600-161002400	Weak transcription	Ovary	ovary
33	chr1:160991600-161007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:160991800-160992000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:160991800-160992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:160991800-160992000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:160991800-160992000	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr1:160991800-160992000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr1:160991800-160992000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:160991800-160992000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr1:160991800-160992000	Enhancers	Fetal Intestine Large	intestine
42	chr1:160991800-160992000	Enhancers	Fetal Intestine Small	intestine
43	chr1:160991800-160992000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr1:160991800-160992200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr1:160991800-160992200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:160991800-160992200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:160991800-160992400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:160991800-160992400	Enhancers	Adipose Nuclei	Adipose
49	chr1:160991800-160992600	Enhancers	Stomach Mucosa	stomach
50	chr1:160991800-160997000	Weak transcription	Primary B cells from peripheral blood	blood

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