Variant report

Variant	rs9828068
Chromosome Location	chr3:136342702-136342703
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136340612..136342191-chr3:136342513..136345195,2	MCF-7	breast:
2	chr3:136342393..136347212-chr3:136468546..136473681,8	MCF-7	breast:
3	chr3:136341644..136343243-chr3:136343703..136345406,2	K562	blood:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13433980	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1484250	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16843991	0.83[AFR][1000 genomes]
rs1872240	0.81[EUR][1000 genomes]
rs28682370	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34962604	0.81[AFR][1000 genomes]
rs35644083	0.82[AFR][1000 genomes]
rs4336059	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402873	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55993001	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047785	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59931907	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6439642	0.83[AFR][1000 genomes]
rs66810260	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6763239	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765239	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771713	0.83[EUR][1000 genomes]
rs6772759	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782151	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6788346	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6789541	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6799699	0.81[EUR][1000 genomes]
rs6800969	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806795	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612160	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7621017	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7621970	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623824	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626418	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7627292	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644346	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7644471	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9818372	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9820513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832572	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9834631	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845950	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9869361	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869957	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876771	0.82[AMR][1000 genomes]
rs9877786	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881078	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
3	chr3:136286800-136343600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:136290000-136351600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:136297200-136345400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:136297200-136351200	Weak transcription	Pancreas	Pancrea
7	chr3:136298600-136351600	Weak transcription	HSMM	muscle
8	chr3:136300200-136351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:136305800-136343800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:136306200-136343400	Weak transcription	HepG2	liver
11	chr3:136308000-136357400	Weak transcription	Lung	lung
12	chr3:136313400-136344000	Weak transcription	Fetal Heart	heart
13	chr3:136315200-136343800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:136315400-136356400	Weak transcription	Brain Anterior Caudate	brain
15	chr3:136315800-136343600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:136315800-136344400	Weak transcription	Small Intestine	intestine
17	chr3:136315800-136346800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:136315800-136355600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:136315800-136361000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:136316000-136364400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:136319000-136344000	Weak transcription	NH-A	brain
22	chr3:136320800-136343800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:136320800-136356800	Weak transcription	Ovary	ovary
24	chr3:136322200-136355200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:136323200-136347000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:136323400-136343400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:136323400-136347200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:136323400-136362000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:136323600-136343800	Weak transcription	Hela-S3	cervix
30	chr3:136323800-136347000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:136324200-136346600	Weak transcription	Primary B cells from cord blood	blood
32	chr3:136324200-136363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:136324400-136343200	Weak transcription	HUVEC	blood vessel
34	chr3:136327400-136357400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:136327600-136343200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:136327600-136343400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:136327800-136346800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:136328000-136344600	Weak transcription	Left Ventricle	heart
39	chr3:136328000-136350200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:136328000-136351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:136328200-136343400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:136328200-136346800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:136330200-136344000	Weak transcription	GM12878-XiMat	blood
44	chr3:136331800-136344000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:136331800-136349400	Weak transcription	NHDF-Ad	bronchial
46	chr3:136331800-136350000	Weak transcription	NHLF	lung
47	chr3:136332800-136344800	Weak transcription	Placenta	Placenta
48	chr3:136333000-136343200	Weak transcription	NHEK	skin
49	chr3:136335000-136344200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr3:136335600-136349800	Weak transcription	Osteobl	bone

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