Variant report

Variant	rs6442038
Chromosome Location	chr3:46960742-46960743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46958432..46960796-chr3:46964876..46966777,2	K562	blood:
2	chr3:46952895..46958117-chr3:46959206..46961896,4	K562	blood:
3	chr3:46959572..46964744-chr3:47019685..47022542,4	K562	blood:
4	chr3:46959005..46961789-chr3:47016255..47019685,3	K562	blood:
5	chr3:46959018..46961280-chr3:47014684..47016373,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1001284	0.85[ASN][1000 genomes]
rs10865943	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1138518	0.86[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11705936	0.89[ASN][1000 genomes]
rs11719795	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1466275	0.83[ASN][1000 genomes]
rs2168443	0.86[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap]
rs2242116	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2290545	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2290546	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4539969	0.83[ASN][1000 genomes]
rs4587	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4682845	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683294	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4683296	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683297	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683298	0.90[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683299	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683300	0.83[ASN][1000 genomes]
rs4683301	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs6442039	0.83[ASN][1000 genomes]
rs6442040	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6780601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs724448	0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs724449	0.86[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs724450	0.91[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7623898	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7635480	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7645278	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7646906	0.85[ASN][1000 genomes]
rs9852082	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9855938	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	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
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	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
10	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6442038	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46950600-46961800	Weak transcription	Aorta	Aorta
2	chr3:46951400-46961600	Weak transcription	Stomach Mucosa	stomach
3	chr3:46951600-46960800	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:46951600-46961800	Weak transcription	HepG2	liver
5	chr3:46951600-46962400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:46955600-46961200	Weak transcription	Gastric	stomach
7	chr3:46955600-46961400	Weak transcription	Small Intestine	intestine
8	chr3:46955800-46961800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:46955800-46961800	Weak transcription	Psoas Muscle	Psoas
10	chr3:46955800-46964800	Weak transcription	Right Atrium	heart
11	chr3:46956000-46962000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:46956400-46965200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:46956600-46967200	Strong transcription	Thymus	Thymus
14	chr3:46956800-46966600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr3:46957000-46964600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:46957000-46965400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr3:46957200-46964800	Weak transcription	Fetal Heart	heart
18	chr3:46957800-46966600	Strong transcription	Fetal Thymus	thymus
19	chr3:46957800-46967200	Strong transcription	HSMM	muscle
20	chr3:46958200-46964800	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr3:46958200-46966800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr3:46958200-46967200	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr3:46958200-46967600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:46958200-46968200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr3:46958200-46968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:46958400-46960800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:46958400-46962600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:46958400-46965200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:46958400-46965200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:46958400-46966800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:46958400-46967200	Strong transcription	HMEC	breast
32	chr3:46958400-46967600	Strong transcription	Primary T cells from cord blood	blood
33	chr3:46958400-46967800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:46958400-46968200	Strong transcription	Dnd41	blood
35	chr3:46958600-46960800	Strong transcription	Brain Germinal Matrix	brain
36	chr3:46958600-46962600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:46958600-46962800	ZNF genes & repeats	GM12878-XiMat	blood
38	chr3:46958600-46963200	Strong transcription	HUVEC	blood vessel
39	chr3:46958600-46964600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:46958600-46964600	Strong transcription	Fetal Brain Male	brain
41	chr3:46958600-46964800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:46958600-46965000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:46958600-46965200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:46958600-46965200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:46958600-46965200	Strong transcription	Fetal Intestine Large	intestine
46	chr3:46958600-46965600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr3:46958600-46966400	Strong transcription	Placenta	Placenta
48	chr3:46958600-46966600	Strong transcription	Adipose Nuclei	Adipose
49	chr3:46958600-46966800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:46958600-46966800	Strong transcription	HSMMtube	muscle

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