Variant report

Variant	rs3735645
Chromosome Location	chr7:117354866-117354867
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 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	chr7:117075650..117077165-chr7:117353827..117356088,2	MCF-7	breast:
6	7:116728195-116740907..7:117341506-117356953	Hela-S3	cervix:
7	7:116434729-116454408..7:117341506-117356953	Hela-S3	cervix:
8	chr7:117101401..117103711-chr7:117353443..117355432,2	MCF-7	breast:
9	7:117114628-117119361..7:117341506-117356953	H1-hESC	embryonic stem cell:	embryo
10	7:117100350-117112126..7:117341506-117356953	GM12878	blood:
11	7:115847372-115857098..7:117341506-117356953	Hela-S3	cervix:
12	7:115890993-115892266..7:117341506-117356953	H1-hESC	embryonic stem cell:	embryo
13	7:116307511-116321259..7:117341506-117356953	Hela-S3	cervix:
14	7:116604327-116608063..7:117341506-117356953	H1-hESC	embryonic stem cell:	embryo
15	7:115861595-115870968..7:117341506-117356953	Hela-S3	cervix:

No data

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

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10266794	0.82[ASN][1000 genomes]
rs1208524	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1208525	0.96[CEU][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1208526	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1208528	0.96[CEU][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs213965	0.84[ASW][hapmap]
rs213971	0.84[ASW][hapmap]
rs213977	0.92[ASW][hapmap];0.85[CEU][hapmap];0.85[CHD][hapmap];0.92[MEX][hapmap]
rs213987	0.81[CHD][hapmap];0.91[MEX][hapmap]
rs214152	0.96[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs214167	0.91[MEX][hapmap]
rs2402229	0.96[CEU][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34445757	0.83[ASN][1000 genomes]
rs6466619	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6970681	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6978581	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]
rs7777807	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7784537	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7793030	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs975722	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3735645	CFTR	cis	cerebellum	SCAN
rs3735645	ING3	cis	parietal	SCAN
rs3735645	PPP1R3A	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

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	chr7:117347600-117356800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:117347600-117366600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:117347800-117363000	Weak transcription	Fetal Heart	heart
8	chr7:117348400-117357000	Weak transcription	Fetal Lung	lung
9	chr7:117349000-117359000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:117349600-117385000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:117350000-117357400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:117350200-117356800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr7:117350200-117356800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr7:117350200-117373800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:117350400-117364600	Weak transcription	NHLF	lung
16	chr7:117350600-117355000	Weak transcription	Hela-S3	cervix
17	chr7:117350600-117357000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr7:117350800-117357200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:117351600-117364600	Weak transcription	Fetal Stomach	stomach
20	chr7:117351800-117355600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:117351800-117356400	Weak transcription	Brain Germinal Matrix	brain
22	chr7:117351800-117366600	Weak transcription	Aorta	Aorta
23	chr7:117352000-117355800	Weak transcription	Fetal Thymus	thymus
24	chr7:117352200-117355800	Weak transcription	Brain Angular Gyrus	brain
25	chr7:117352400-117364800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:117352600-117355800	Weak transcription	Brain Substantia Nigra	brain
27	chr7:117352600-117356600	Enhancers	Dnd41	blood
28	chr7:117352800-117368000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:117353200-117357600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:117353200-117384600	Weak transcription	Ovary	ovary
31	chr7:117353400-117362200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:117353400-117367800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:117354000-117355000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:117354000-117355400	Strong transcription	Brain Anterior Caudate	brain
35	chr7:117354000-117356400	Weak transcription	Pancreas	Pancrea
36	chr7:117354000-117361600	Strong transcription	Fetal Brain Female	brain
37	chr7:117354200-117355000	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr7:117354600-117355000	Strong transcription	Adipose Nuclei	Adipose
39	chr7:117354600-117355200	Strong transcription	Brain Hippocampus Middle	brain
40	chr7:117354600-117373800	Weak transcription	Esophagus	oesophagus
41	chr7:117354800-117355000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr7:117354800-117356400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:117354800-117417200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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