Variant report

Variant	rs7624084
Chromosome Location	chr3:141093285-141093286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141092073..141094472-chr3:141095647..141097319,2	MCF-7	breast:
2	chr3:141083461..141090540-chr3:141091667..141099186,10	MCF-7	breast:
3	chr3:141091576..141094274-chr3:141094633..141097047,3	K562	blood:
4	chr3:141091576..141094274-chr3:141094633..141096791,2	K562	blood:
5	chr3:141086015..141089239-chr3:141089534..141093928,5	K562	blood:
6	chr3:141091574..141093729-chr3:141119134..141120872,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13068733	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1344672	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1344674	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1346408	0.93[CEU][hapmap]
rs1582874	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs1863868	0.93[CEU][hapmap]
rs1991431	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs2871960	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683605	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4683606	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57345461	0.89[ASN][1000 genomes]
rs58473751	0.89[ASN][1000 genomes]
rs6440001	0.89[CEU][hapmap]
rs6440003	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440006	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6762826	0.90[JPT][hapmap]
rs6763927	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6763931	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6764769	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6784404	0.85[CEU][hapmap]
rs6785012	0.87[EUR][1000 genomes]
rs6802753	0.84[JPT][hapmap]
rs6808936	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs724016	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7613516	0.93[CEU][hapmap]
rs7632381	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7650602	0.80[ASN][1000 genomes]
rs9846396	0.89[CEU][hapmap]
rs9853018	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9856584	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9866391	0.83[CEU][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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141085800-141094200	Weak transcription	Spleen	Spleen
2	chr3:141086000-141093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:141087000-141107800	Weak transcription	Pancreas	Pancrea
4	chr3:141088000-141102400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:141088000-141105200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:141088200-141094200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:141088200-141094400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:141088200-141095000	Weak transcription	Colonic Mucosa	Colon
9	chr3:141088200-141101800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:141088200-141102400	Weak transcription	Fetal Kidney	kidney
11	chr3:141088400-141094200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:141088400-141102400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:141088400-141107600	Weak transcription	Small Intestine	intestine
14	chr3:141088600-141094200	Weak transcription	Ovary	ovary
15	chr3:141088800-141094200	Weak transcription	Right Ventricle	heart
16	chr3:141089000-141094600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:141089200-141094200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:141089200-141094400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:141089200-141094400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:141089200-141094400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:141089200-141094600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:141089200-141095000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:141089200-141095200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:141089200-141096200	Weak transcription	Fetal Lung	lung
25	chr3:141089200-141097600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:141089200-141097600	Weak transcription	Adipose Nuclei	Adipose
27	chr3:141089200-141098800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:141089200-141099000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:141089200-141101800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:141089200-141101800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:141089200-141104800	Strong transcription	Fetal Intestine Large	intestine
32	chr3:141089200-141115800	Weak transcription	Psoas Muscle	Psoas
33	chr3:141089400-141094600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:141089400-141102200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:141089400-141104200	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:141089600-141094400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:141089600-141094800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:141089600-141096000	Genic enhancers	A549	lung
39	chr3:141089600-141099000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:141089600-141102400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:141089600-141102400	Weak transcription	Fetal Brain Male	brain
42	chr3:141089600-141102400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:141089600-141105600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:141089800-141094000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:141089800-141094200	Weak transcription	Aorta	Aorta
46	chr3:141089800-141094600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr3:141089800-141094600	Weak transcription	HUVEC	blood vessel
48	chr3:141089800-141097600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:141089800-141097800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:141089800-141099200	Weak transcription	Brain Anterior Caudate	brain

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