Variant report

Variant	rs6414436
Chromosome Location	chr3:47133172-47133173
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47132552..47135430-chr4:99181740..99183260,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214559	Chromatin interaction
ENSG00000138698	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10433549	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130114	0.85[EUR][1000 genomes]
rs11130115	0.84[EUR][1000 genomes]
rs11707736	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708451	0.84[EUR][1000 genomes]
rs11709660	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11712716	0.84[EUR][1000 genomes]
rs11713693	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11714373	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11715121	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11716539	0.84[EUR][1000 genomes]
rs11718795	0.83[EUR][1000 genomes]
rs11719306	0.84[EUR][1000 genomes]
rs11719738	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11720139	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11917361	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11920354	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11923706	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488225	0.81[EUR][1000 genomes]
rs12489211	0.82[EUR][1000 genomes]
rs12493425	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629262	0.84[EUR][1000 genomes]
rs12631730	0.87[ASN][1000 genomes]
rs12635619	0.81[EUR][1000 genomes]
rs12715421	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061071	0.88[EUR][1000 genomes]
rs13062022	0.85[EUR][1000 genomes]
rs13084117	0.84[EUR][1000 genomes]
rs13091054	0.84[EUR][1000 genomes]
rs13094672	0.84[EUR][1000 genomes]
rs13098228	0.88[EUR][1000 genomes]
rs1466740	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1466741	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17784127	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1811652	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278963	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305635	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34103310	0.83[EUR][1000 genomes]
rs4018905	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078466	0.87[EUR][1000 genomes]
rs4082155	0.87[EUR][1000 genomes]
rs4682852	0.84[EUR][1000 genomes]
rs4683320	0.84[EUR][1000 genomes]
rs4683322	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55724164	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55927279	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56217494	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56249396	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57756484	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58956475	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62246398	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62246402	0.82[AFR][1000 genomes]
rs62246451	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62246455	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62248905	0.82[AFR][1000 genomes]
rs6414435	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442055	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442059	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442060	0.85[ASN][1000 genomes]
rs6763236	0.84[EUR][1000 genomes]
rs6766230	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6767218	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6767907	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6768722	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6772670	0.84[EUR][1000 genomes]
rs6773521	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6777145	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781941	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6785790	0.85[EUR][1000 genomes]
rs6791062	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794193	0.85[EUR][1000 genomes]
rs7373821	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7426969	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7433300	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749511	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs749512	0.91[ASN][1000 genomes]
rs7610620	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7615323	0.81[EUR][1000 genomes]
rs7620997	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7621911	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7623888	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625067	0.84[EUR][1000 genomes]
rs7625070	0.84[EUR][1000 genomes]
rs7632501	0.82[AFR][1000 genomes]
rs7633435	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9311403	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812878	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9818382	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9821119	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837343	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9843075	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9844122	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845728	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854790	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858443	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9875235	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1002970	chr3:47120592-47170607	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6414436	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs6414436	SETD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47083200-47135200	Weak transcription	Small Intestine	intestine
2	chr3:47083400-47138600	Weak transcription	Psoas Muscle	Psoas
3	chr3:47098800-47149600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:47101400-47147800	Strong transcription	Dnd41	blood
5	chr3:47110200-47150200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47110400-47133200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:47110600-47148000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:47111000-47147600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:47112400-47153600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:47114600-47147800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:47114800-47137600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:47115400-47147800	Strong transcription	Fetal Thymus	thymus
13	chr3:47117600-47148600	Strong transcription	Placenta	Placenta
14	chr3:47118200-47139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:47118200-47148600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:47118400-47140600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:47118600-47143400	Weak transcription	Fetal Heart	heart
18	chr3:47120200-47135600	Weak transcription	A549	lung
19	chr3:47121600-47133800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr3:47122600-47143600	Weak transcription	Right Ventricle	heart
21	chr3:47122800-47138800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:47123000-47136000	Weak transcription	HSMMtube	muscle
23	chr3:47123000-47159200	Weak transcription	Brain Substantia Nigra	brain
24	chr3:47124600-47137600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:47124600-47154400	Weak transcription	Fetal Brain Male	brain
26	chr3:47124800-47138600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:47125600-47140600	Strong transcription	Primary B cells from cord blood	blood
28	chr3:47125600-47154600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:47125800-47133800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:47125800-47134400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:47125800-47135200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:47125800-47135200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:47125800-47135200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:47125800-47135800	Weak transcription	Fetal Kidney	kidney
35	chr3:47125800-47136200	Weak transcription	Ovary	ovary
36	chr3:47125800-47137200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:47125800-47137600	Weak transcription	Brain Anterior Caudate	brain
38	chr3:47125800-47138600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:47125800-47138600	Weak transcription	Brain Germinal Matrix	brain
40	chr3:47125800-47150000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:47125800-47153600	Weak transcription	Esophagus	oesophagus
42	chr3:47125800-47154600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:47125800-47154600	Weak transcription	Gastric	stomach
44	chr3:47125800-47155000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:47126000-47153600	Weak transcription	Aorta	Aorta
46	chr3:47126400-47159800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:47126800-47168200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:47127000-47142800	Weak transcription	Brain Angular Gyrus	brain
49	chr3:47127800-47133400	Weak transcription	NHDF-Ad	bronchial
50	chr3:47127800-47135600	Weak transcription	Brain Cingulate Gyrus	brain

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