Variant report

Variant	rs1491170
Chromosome Location	chr3:56627598-56627599
allele	C/T
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	GATA3	chr3:56627441-56627733	T-47D	breast:	n/a	n/a
2	FOXA1	chr3:56627522-56627727	T-47D	breast:	n/a	chr3:56627594-56627609

Variant related genes	Relation type
CCDC66	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11130525	0.84[YRI][hapmap]
rs11130526	0.85[YRI][hapmap]
rs11549487	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926770	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs282535	1.00[ASW][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4299454	0.87[AMR][1000 genomes]
rs4974219	0.87[AMR][1000 genomes]
rs59285806	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6796679	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7619518	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630094	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7635349	1.00[ASW][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637301	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311608	1.00[EUR][1000 genomes]
rs9879536	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv528087	chr3:56608033-56628031	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
2	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
3	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
4	chr3:56600600-56640000	Weak transcription	NHLF	lung
5	chr3:56603000-56631600	Weak transcription	Fetal Brain Male	brain
6	chr3:56603200-56650400	Weak transcription	K562	blood
7	chr3:56603600-56640000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:56604200-56627600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:56604600-56627600	Weak transcription	HUVEC	blood vessel
10	chr3:56605600-56639600	Weak transcription	Pancreas	Pancrea
11	chr3:56605800-56639400	Weak transcription	Spleen	Spleen
12	chr3:56605800-56639600	Weak transcription	Esophagus	oesophagus
13	chr3:56606000-56627600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:56606000-56627600	Weak transcription	Left Ventricle	heart
15	chr3:56606000-56629200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
17	chr3:56606600-56627800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:56606800-56627600	Weak transcription	Osteobl	bone
19	chr3:56607800-56627600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:56607800-56627600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:56607800-56627600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:56607800-56627600	Weak transcription	NHDF-Ad	bronchial
23	chr3:56607800-56627800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:56607800-56629800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:56607800-56639800	Weak transcription	HSMMtube	muscle
26	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
27	chr3:56608200-56627600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:56609400-56638600	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:56610000-56627600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:56610000-56627600	Weak transcription	HSMM	muscle
31	chr3:56616200-56633800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:56616400-56639400	Weak transcription	Lung	lung
33	chr3:56617200-56627600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:56617200-56627600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:56617200-56629000	Weak transcription	Fetal Brain Female	brain
36	chr3:56617200-56629400	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:56617200-56629400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:56617200-56629800	Weak transcription	Hela-S3	cervix
39	chr3:56617200-56630000	Weak transcription	Fetal Stomach	stomach
40	chr3:56617200-56639200	Weak transcription	Thymus	Thymus
41	chr3:56617200-56639600	Weak transcription	Aorta	Aorta
42	chr3:56617400-56627600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:56617400-56627600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:56617400-56627600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:56617400-56627600	Weak transcription	Adipose Nuclei	Adipose
46	chr3:56617400-56627600	Weak transcription	Fetal Kidney	kidney
47	chr3:56617400-56629400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:56617400-56639800	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:56617400-56639800	Weak transcription	Dnd41	blood
50	chr3:56618600-56627800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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