Variant report

Variant	rs6978581
Chromosome Location	chr7:117356893-117356894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:117065049-117068137..7:117341506-117356953	H1-hESC	embryonic stem cell:	embryo
2	7:116651084-116657331..7:117341506-117356953	Hela-S3	cervix:
3	7:117251668-117255413..7:117341506-117356953	Hela-S3	cervix:
4	7:116754962-116765597..7:117341506-117356953	Hela-S3	cervix:
5	7:116728195-116740907..7:117341506-117356953	Hela-S3	cervix:
6	7:116434729-116454408..7:117341506-117356953	Hela-S3	cervix:
7	7:117114628-117119361..7:117341506-117356953	H1-hESC	embryonic stem cell:	embryo
8	7:117100350-117112126..7:117341506-117356953	GM12878	blood:
9	7:115847372-115857098..7:117341506-117356953	Hela-S3	cervix:
10	7:115890993-115892266..7:117341506-117356953	H1-hESC	embryonic stem cell:	embryo
11	7:116307511-116321259..7:117341506-117356953	Hela-S3	cervix:
12	7:116604327-116608063..7:117341506-117356953	H1-hESC	embryonic stem cell:	embryo
13	7:115861595-115870968..7:117341506-117356953	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000228368	Chromatin interaction
ENSG00000001626	Chromatin interaction
ENSG00000154438	Chromatin interaction
ENSG00000004866	Chromatin interaction
ENSG00000135269	Chromatin interaction
ENSG00000105976	Chromatin interaction
ENSG00000198898	Chromatin interaction
ENSG00000226367	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10266794	0.92[ASN][1000 genomes]
rs1208524	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1208525	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1208526	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1208528	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534186	0.89[CHB][hapmap]
rs12672572	0.84[ASN][1000 genomes]
rs13237279	0.81[ASN][1000 genomes]
rs177284	0.84[ASN][1000 genomes]
rs1896885	0.88[ASN][1000 genomes]
rs2106155	0.84[CHB][hapmap]
rs213965	0.84[ASW][hapmap]
rs213971	0.84[ASW][hapmap]
rs213977	0.92[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.92[MEX][hapmap]
rs213985	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs213987	0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs214152	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214160	0.86[ASN][1000 genomes]
rs214161	0.85[ASN][1000 genomes]
rs214167	0.89[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs2237726	0.89[CHB][hapmap]
rs2246450	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2254742	0.89[CHB][hapmap]
rs2283058	0.89[CHB][hapmap]
rs2299445	0.89[CHB][hapmap]
rs2402229	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34257228	0.88[ASN][1000 genomes]
rs34445757	0.93[ASN][1000 genomes]
rs3735645	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4148724	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs4373465	0.88[ASN][1000 genomes]
rs6466619	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6970681	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6975912	0.81[ASN][1000 genomes]
rs7777807	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7784537	0.94[JPT][hapmap]
rs7793030	0.88[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7797932	0.89[CHB][hapmap]
rs975722	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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	nsv464695	chr7:117342771-117393516	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv608258	chr7:117342771-117393516	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6978581	CFTR	cis	cerebellum	SCAN
rs6978581	ING3	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117327000-117376400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:117344400-117364400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:117346600-117373400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:117347000-117358000	Weak transcription	Fetal Brain Male	brain
5	chr7:117347600-117366600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:117347800-117363000	Weak transcription	Fetal Heart	heart
7	chr7:117348400-117357000	Weak transcription	Fetal Lung	lung
8	chr7:117349000-117359000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:117349600-117385000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:117350000-117357400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:117350200-117373800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:117350400-117364600	Weak transcription	NHLF	lung
13	chr7:117350600-117357000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:117350800-117357200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:117351600-117364600	Weak transcription	Fetal Stomach	stomach
16	chr7:117351800-117366600	Weak transcription	Aorta	Aorta
17	chr7:117352400-117364800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:117352800-117368000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:117353200-117357600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:117353200-117384600	Weak transcription	Ovary	ovary
21	chr7:117353400-117362200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:117353400-117367800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:117354000-117361600	Strong transcription	Fetal Brain Female	brain
24	chr7:117354600-117373800	Weak transcription	Esophagus	oesophagus
25	chr7:117354800-117417200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr7:117355000-117357000	Weak transcription	Adipose Nuclei	Adipose
27	chr7:117355000-117357200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr7:117355000-117382800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr7:117355600-117357600	Enhancers	Duodenum Mucosa	Duodenum
30	chr7:117355800-117357400	Enhancers	Brain Substantia Nigra	brain
31	chr7:117355800-117357800	Enhancers	Fetal Intestine Large	intestine
32	chr7:117355800-117358400	Enhancers	Fetal Intestine Small	intestine
33	chr7:117355800-117358400	Enhancers	Stomach Mucosa	stomach
34	chr7:117355800-117359400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr7:117355800-117369400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr7:117356000-117357000	Weak transcription	A549	lung
37	chr7:117356000-117357400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:117356200-117431400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr7:117356400-117357200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:117356400-117357200	Genic enhancers	Brain Hippocampus Middle	brain
41	chr7:117356400-117357200	Enhancers	Pancreas	Pancrea
42	chr7:117356400-117358000	Weak transcription	Brain Angular Gyrus	brain
43	chr7:117356400-117358800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:117356600-117357000	Weak transcription	Brain Anterior Caudate	brain
45	chr7:117356600-117357600	Weak transcription	Fetal Kidney	kidney
46	chr7:117356800-117357200	Enhancers	Liver	Liver
47	chr7:117356800-117357600	Strong transcription	Brain Germinal Matrix	brain
48	chr7:117356800-117357800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr7:117356800-117360200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr7:117356800-117362000	Strong transcription	H1 Cell Line	embryonic stem cell

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