Variant report

Variant	rs59865540
Chromosome Location	chr3:156863213-156863214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156851307..156853070-chr3:156861254..156863346,2	MCF-7	breast:
2	chr3:156476830..156479789-chr3:156862694..156865587,2	K562	blood:
3	chr3:156397092..156399511-chr3:156863031..156865658,2	MCF-7	breast:
4	chr3:156826801..156832803-chr3:156862347..156866322,5	K562	blood:
5	chr3:156533203..156535448-chr3:156862517..156864501,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000240875	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10936061	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936062	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936063	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936064	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936065	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936066	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936067	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10936068	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10936069	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10936074	0.81[EUR][1000 genomes]
rs12488480	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12489453	0.82[EUR][1000 genomes]
rs12489799	0.84[EUR][1000 genomes]
rs12490836	0.85[EUR][1000 genomes]
rs12492801	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496051	0.82[EUR][1000 genomes]
rs12496111	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12497891	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12630209	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12634818	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12635088	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12636125	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16827318	0.82[EUR][1000 genomes]
rs16827352	0.81[EUR][1000 genomes]
rs17552941	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1995304	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2321740	0.81[EUR][1000 genomes]
rs35910014	0.82[EUR][1000 genomes]
rs3935750	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41272613	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4371471	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4383467	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4413278	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4608646	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4679788	0.82[EUR][1000 genomes]
rs4680340	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680343	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680345	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5003893	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55828309	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55835412	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55949516	0.85[EUR][1000 genomes]
rs55953639	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56078410	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56263456	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57322659	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57511361	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59210914	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59279023	0.81[EUR][1000 genomes]
rs59485606	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60153077	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61149035	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62274129	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62274155	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62274156	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62274159	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276460	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276461	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276462	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276465	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62276470	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62276471	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62276474	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62276475	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62276479	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62276480	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62276488	0.83[ASN][1000 genomes]
rs62276489	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62276490	0.86[EUR][1000 genomes]
rs62276491	0.86[EUR][1000 genomes]
rs62276495	0.86[EUR][1000 genomes]
rs62276496	0.86[EUR][1000 genomes]
rs62276497	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62276501	0.84[EUR][1000 genomes]
rs62276502	0.84[EUR][1000 genomes]
rs62276504	0.82[EUR][1000 genomes]
rs62276505	0.81[EUR][1000 genomes]
rs6441115	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6441116	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6441119	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6768052	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6768074	0.81[EUR][1000 genomes]
rs6780205	0.81[EUR][1000 genomes]
rs6781682	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6792479	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6805989	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6806232	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6809307	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154633	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73154649	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73154657	0.85[EUR][1000 genomes]
rs73154659	0.82[EUR][1000 genomes]
rs73873800	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7621912	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7626589	0.84[EUR][1000 genomes]
rs7633004	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7648599	0.84[EUR][1000 genomes]
rs8180056	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8180057	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8925	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][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	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156848400-156866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:156848400-156866000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:156848600-156876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:156849800-156864000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:156852600-156873400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:156853200-156865400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:156853400-156872000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:156855000-156865800	Weak transcription	Aorta	Aorta
9	chr3:156855000-156866000	Weak transcription	Ovary	ovary
10	chr3:156855000-156872000	Weak transcription	Right Atrium	heart
11	chr3:156855400-156865400	Weak transcription	Fetal Brain Male	brain
12	chr3:156855400-156865800	Weak transcription	Colonic Mucosa	Colon
13	chr3:156855400-156866000	Weak transcription	Fetal Heart	heart
14	chr3:156855400-156877000	Weak transcription	Gastric	stomach
15	chr3:156855600-156863600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:156855600-156863600	Weak transcription	Brain Angular Gyrus	brain
17	chr3:156855600-156864200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:156855600-156865400	Weak transcription	HepG2	liver
19	chr3:156855600-156865800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:156855600-156865800	Weak transcription	NHLF	lung
21	chr3:156855600-156866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:156855600-156867200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:156855800-156865800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:156855800-156867400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:156856000-156863800	Weak transcription	Stomach Mucosa	stomach
26	chr3:156856000-156870800	Strong transcription	Primary T cells from cord blood	blood
27	chr3:156856000-156874600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:156857200-156864000	Strong transcription	Left Ventricle	heart
29	chr3:156858000-156871200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:156858000-156872000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr3:156858200-156870400	Strong transcription	Liver	Liver
32	chr3:156858200-156871200	Strong transcription	Adipose Nuclei	Adipose
33	chr3:156858400-156876400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:156858600-156871200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr3:156858600-156871200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr3:156858600-156872200	Strong transcription	Primary B cells from cord blood	blood
37	chr3:156858600-156872400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:156858800-156865000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:156859000-156871800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:156859200-156866600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:156859200-156869600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:156859200-156870800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:156859400-156872200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:156859400-156872400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:156859400-156876200	Strong transcription	Placenta	Placenta
46	chr3:156859800-156863600	Strong transcription	Fetal Intestine Large	intestine
47	chr3:156859800-156871600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:156859800-156871800	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:156860000-156867200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:156860000-156871000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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