Variant report

Variant	rs6442060
Chromosome Location	chr3:47192764-47192765
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47192656..47195424-chr3:47287048..47290020,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11707736	0.82[ASN][1000 genomes]
rs11709660	0.81[ASN][1000 genomes]
rs11713693	0.81[ASN][1000 genomes]
rs11714373	0.82[ASN][1000 genomes]
rs11715121	0.83[ASN][1000 genomes]
rs11719738	0.86[ASN][1000 genomes]
rs11917361	0.83[ASN][1000 genomes]
rs11923706	0.85[ASN][1000 genomes]
rs12493425	0.88[ASN][1000 genomes]
rs12631730	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12715421	0.84[ASN][1000 genomes]
rs17784127	0.81[ASN][1000 genomes]
rs1811652	0.82[ASN][1000 genomes]
rs4018905	0.86[ASN][1000 genomes]
rs4683322	0.84[ASN][1000 genomes]
rs55927279	0.81[ASN][1000 genomes]
rs56249396	0.81[ASN][1000 genomes]
rs58956475	0.80[ASN][1000 genomes]
rs59299766	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60965459	0.90[ASN][1000 genomes]
rs62246398	0.81[ASN][1000 genomes]
rs62246451	0.82[ASN][1000 genomes]
rs6414435	0.85[ASN][1000 genomes]
rs6414436	0.85[ASN][1000 genomes]
rs6442055	0.85[ASN][1000 genomes]
rs6442059	0.88[ASN][1000 genomes]
rs6766230	0.86[ASN][1000 genomes]
rs6767218	0.81[ASN][1000 genomes]
rs6767907	0.88[ASN][1000 genomes]
rs6768722	0.84[ASN][1000 genomes]
rs6777145	0.85[ASN][1000 genomes]
rs6791062	0.88[ASN][1000 genomes]
rs7433300	0.85[ASN][1000 genomes]
rs7610620	0.82[ASN][1000 genomes]
rs7620997	0.82[ASN][1000 genomes]
rs7633435	0.82[ASN][1000 genomes]
rs9311403	0.86[ASN][1000 genomes]
rs9812878	0.88[ASN][1000 genomes]
rs9818382	0.86[ASN][1000 genomes]
rs9821119	0.85[ASN][1000 genomes]
rs9837343	0.88[ASN][1000 genomes]
rs9843075	0.94[ASN][1000 genomes]
rs9844122	0.85[ASN][1000 genomes]
rs9845728	0.85[ASN][1000 genomes]
rs9854790	0.84[ASN][1000 genomes]
rs9858443	0.84[ASN][1000 genomes]
rs9875235	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6442060	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47165800-47197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:47166000-47200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:47166000-47201200	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:47166000-47204600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:47166200-47197200	Weak transcription	Aorta	Aorta
6	chr3:47166200-47200600	Weak transcription	Hela-S3	cervix
7	chr3:47166400-47194200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:47166600-47204200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:47167400-47202400	Weak transcription	HSMM	muscle
10	chr3:47167800-47195400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:47175800-47200400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:47177800-47194200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:47178000-47194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:47181000-47193600	Weak transcription	Fetal Heart	heart
15	chr3:47182000-47195400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:47182600-47200800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:47182800-47198200	Weak transcription	Primary B cells from cord blood	blood
18	chr3:47183600-47193800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:47183600-47200800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:47183600-47202200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:47183800-47193800	Weak transcription	Primary T cells from cord blood	blood
22	chr3:47183800-47194000	Weak transcription	Dnd41	blood
23	chr3:47183800-47194200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:47183800-47194400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:47183800-47198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:47183800-47202200	Weak transcription	NHEK	skin
27	chr3:47183800-47203000	Weak transcription	Colonic Mucosa	Colon
28	chr3:47184000-47194200	Weak transcription	Spleen	Spleen
29	chr3:47184000-47197000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:47184400-47198400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:47184600-47194200	Weak transcription	Fetal Thymus	thymus
32	chr3:47184600-47194200	Weak transcription	Psoas Muscle	Psoas
33	chr3:47184600-47198000	Weak transcription	Thymus	Thymus
34	chr3:47184600-47202200	Weak transcription	Esophagus	oesophagus
35	chr3:47184800-47194000	Weak transcription	Ovary	ovary
36	chr3:47184800-47194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:47184800-47197000	Weak transcription	Gastric	stomach
38	chr3:47184800-47199600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:47184800-47199800	Weak transcription	Fetal Intestine Small	intestine
40	chr3:47185000-47193400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:47186000-47194000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:47186800-47197000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:47187400-47193000	Weak transcription	Lung	lung
44	chr3:47187400-47193600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:47187400-47197200	Weak transcription	Right Atrium	heart
46	chr3:47187800-47195000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:47188400-47200800	Weak transcription	Fetal Stomach	stomach
48	chr3:47188600-47202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:47189600-47195400	Enhancers	HepG2	liver
50	chr3:47190000-47196000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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