Variant report

Variant	rs62246375
Chromosome Location	chr3:47014464-47014465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47007836..47011318-chr3:47011441..47014509,4	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10433549	0.87[EUR][1000 genomes]
rs10461018	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1079276	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1108301	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11130110	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130111	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130112	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11709660	0.81[EUR][1000 genomes]
rs11715121	0.81[EUR][1000 genomes]
rs11716553	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11720139	0.87[EUR][1000 genomes]
rs11917361	0.83[EUR][1000 genomes]
rs11917474	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12152493	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12491473	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12630534	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12715421	0.82[EUR][1000 genomes]
rs13062681	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13066214	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13077398	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091054	0.86[EUR][1000 genomes]
rs1463393	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17784127	0.85[EUR][1000 genomes]
rs1869869	0.99[EUR][1000 genomes]
rs1869871	0.90[EUR][1000 genomes]
rs2061197	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278963	0.88[EUR][1000 genomes]
rs2305634	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2305635	0.88[EUR][1000 genomes]
rs2305638	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2385867	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34103310	0.88[EUR][1000 genomes]
rs34344887	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4078466	0.84[EUR][1000 genomes]
rs4082155	0.85[EUR][1000 genomes]
rs4234465	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4682831	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4682837	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682844	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683322	0.81[EUR][1000 genomes]
rs55724164	0.83[EUR][1000 genomes]
rs55843455	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55927279	0.82[EUR][1000 genomes]
rs56217494	0.84[EUR][1000 genomes]
rs56249396	0.82[EUR][1000 genomes]
rs61729713	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62246398	0.83[EUR][1000 genomes]
rs62248439	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442055	0.81[EUR][1000 genomes]
rs66539935	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66564457	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6763236	0.88[EUR][1000 genomes]
rs6767218	0.83[EUR][1000 genomes]
rs6768722	0.80[EUR][1000 genomes]
rs6774733	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6777145	0.81[EUR][1000 genomes]
rs6794193	0.87[EUR][1000 genomes]
rs6808742	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749511	0.88[EUR][1000 genomes]
rs7610636	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7617689	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7625067	0.88[EUR][1000 genomes]
rs7625070	0.88[EUR][1000 genomes]
rs7628747	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633698	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7636252	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637302	0.85[EUR][1000 genomes]
rs7640397	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854790	0.81[EUR][1000 genomes]
rs9858443	0.82[EUR][1000 genomes]
rs9875235	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
9	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62246375	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs62246375	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47003200-47015800	Weak transcription	Fetal Brain Male	brain
2	chr3:47003200-47016800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:47004800-47017200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:47004800-47017200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:47006600-47017000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:47006800-47014600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:47007000-47017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:47007200-47017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:47007600-47014600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:47007600-47014800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:47007600-47016200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:47007600-47017200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:47007600-47017200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:47007600-47017400	Weak transcription	HSMMtube	muscle
15	chr3:47008200-47014600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:47008400-47015600	Weak transcription	Hela-S3	cervix
17	chr3:47009200-47017200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:47009400-47014800	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr3:47010600-47015400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:47011200-47014600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr3:47011200-47015600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:47011200-47017200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:47011200-47017200	Weak transcription	Aorta	Aorta
24	chr3:47011400-47016200	Weak transcription	HMEC	breast
25	chr3:47012000-47014600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:47012200-47015800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:47012600-47014600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:47012600-47016000	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:47012800-47015800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:47012800-47017200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:47013000-47015600	Weak transcription	Colonic Mucosa	Colon
32	chr3:47013000-47015600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:47013000-47015800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr3:47013000-47015800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:47013000-47015800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:47013000-47015800	Enhancers	Liver	Liver
37	chr3:47013000-47015800	Weak transcription	Brain Germinal Matrix	brain
38	chr3:47013000-47015800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:47013000-47015800	Enhancers	HepG2	liver
40	chr3:47013000-47015800	Weak transcription	NHDF-Ad	bronchial
41	chr3:47013000-47016200	Weak transcription	NHLF	lung
42	chr3:47013000-47016400	Weak transcription	Fetal Brain Female	brain
43	chr3:47013200-47014800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:47013200-47015600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:47013200-47015800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:47013200-47016200	Weak transcription	Osteobl	bone
47	chr3:47013200-47017400	Weak transcription	Fetal Kidney	kidney
48	chr3:47013400-47014600	Genic enhancers	K562	blood
49	chr3:47013400-47014800	Enhancers	Primary T cells from cord blood	blood
50	chr3:47013400-47015200	Weak transcription	Right Atrium	heart

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