Variant report

Variant	rs3808220
Chromosome Location	chr7:116763336-116763337
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	7:116547624-116551247..7:116754962-116765597	GM12878	blood:
2	7:116754962-116765597..7:116894301-116914960	Hela-S3	cervix:
3	7:116245779-116258944..7:116754962-116765597	Hela-S3	cervix:
4	chr7:116721583..116724319-chr7:116761675..116764587,2	MCF-7	breast:
5	chr7:116628498..116630174-chr7:116762682..116764395,2	MCF-7	breast:
6	7:116610596-116619447..7:116754962-116765597	GM12878	blood:
7	chr7:116622535..116624065-chr7:116762723..116764225,2	MCF-7	breast:
8	chr7:116624725..116627030-chr7:116763333..116766148,3	K562	blood:
9	7:116580605-116585719..7:116754962-116765597	GM12878	blood:
10	chr7:116592433..116594260-chr7:116761338..116764255,2	MCF-7	breast:
11	chr7:116592456..116594702-chr7:116762871..116765221,3	MCF-7	breast:
12	7:116754962-116765597..7:117341506-117356953	Hela-S3	cervix:
13	chr7:116571244..116573563-chr7:116761792..116763514,2	MCF-7	breast:
14	chr7:116592383..116595256-chr7:116761894..116764573,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198898	Chromatin interaction
ENSG00000004866	Chromatin interaction
ENSG00000224042	Chromatin interaction
ENSG00000231210	Chromatin interaction
ENSG00000230785	Chromatin interaction
ENSG00000227199	Chromatin interaction
ENSG00000230605	Chromatin interaction
ENSG00000001626	Chromatin interaction
ENSG00000214188	Chromatin interaction
ENSG00000252115	Chromatin interaction
ENSG00000222150	Chromatin interaction
ENSG00000213050	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10228703	0.93[YRI][hapmap]
rs10236117	0.80[AFR][1000 genomes]
rs10251673	1.00[YRI][hapmap]
rs10259701	0.92[YRI][hapmap]
rs10262342	0.92[YRI][hapmap]
rs10266895	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[ASN][1000 genomes]
rs10275342	0.81[ASW][hapmap];0.90[LWK][hapmap];0.93[YRI][hapmap]
rs16870030	1.00[CEU][hapmap]
rs17139321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17139357	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17139383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs17438522	0.86[YRI][hapmap]
rs2301996	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs3758628	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs3808217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3808221	0.81[GIH][hapmap]
rs73477374	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv831108	chr7:116749534-116952011	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116725400-116766400	Weak transcription	Brain Germinal Matrix	brain
2	chr7:116738400-116774200	Weak transcription	Ovary	ovary
3	chr7:116738400-116779600	Weak transcription	Esophagus	oesophagus
4	chr7:116738800-116763400	Weak transcription	Hela-S3	cervix
5	chr7:116745600-116763600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:116750800-116764600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:116751400-116763400	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:116751400-116763600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:116751400-116764600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:116751400-116764600	Weak transcription	Lung	lung
11	chr7:116751400-116778600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr7:116751800-116763800	Weak transcription	Fetal Intestine Small	intestine
13	chr7:116751800-116764400	Weak transcription	Fetal Intestine Large	intestine
14	chr7:116752000-116764600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:116752000-116764600	Weak transcription	Left Ventricle	heart
16	chr7:116754200-116764400	Weak transcription	HSMM	muscle
17	chr7:116754200-116764600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:116754200-116764600	Weak transcription	Aorta	Aorta
19	chr7:116754200-116797400	Weak transcription	Fetal Stomach	stomach
20	chr7:116754600-116763400	Weak transcription	Fetal Heart	heart
21	chr7:116755200-116772000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:116755400-116764600	Weak transcription	Fetal Muscle Leg	muscle
23	chr7:116755400-116764600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr7:116758600-116764400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:116759000-116763400	Weak transcription	Brain Anterior Caudate	brain
26	chr7:116759200-116764600	Weak transcription	Brain Hippocampus Middle	brain
27	chr7:116759200-116766200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:116759200-116778200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:116759400-116763400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:116759400-116765000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:116759400-116766000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:116759600-116764600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:116759600-116764800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:116759600-116765000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr7:116759600-116765200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:116759600-116774200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:116759800-116763600	Weak transcription	Brain Angular Gyrus	brain
38	chr7:116759800-116764600	Weak transcription	Brain Substantia Nigra	brain
39	chr7:116759800-116764800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:116760000-116763400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:116760200-116764800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr7:116760600-116764200	Weak transcription	GM12878-XiMat	blood
43	chr7:116760600-116764600	Weak transcription	HSMMtube	muscle
44	chr7:116760800-116763400	Weak transcription	K562	blood
45	chr7:116761000-116764400	Weak transcription	Liver	Liver
46	chr7:116761200-116763600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:116761200-116771200	Weak transcription	Fetal Brain Female	brain
48	chr7:116761400-116763800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:116762000-116764600	Weak transcription	Placenta	Placenta
50	chr7:116762200-116765200	Enhancers	Placenta Amnion	Placenta Amnion

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