Variant report

Variant	rs1138518
Chromosome Location	chr3:46944274-46944275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46944179..46947066-chr3:46954908..46956436,2	K562	blood:
2	chr3:46746470..46747089-chr3:46944228..46945196,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1001284	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10461018	0.82[JPT][hapmap];0.93[MKK][hapmap]
rs10865943	0.92[ASN][1000 genomes]
rs11130110	0.82[JPT][hapmap]
rs11130111	0.81[JPT][hapmap]
rs11705936	0.92[ASN][1000 genomes]
rs11719795	0.86[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1466275	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061197	0.82[JPT][hapmap];0.82[LWK][hapmap]
rs2168443	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2242116	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290545	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2290546	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4539969	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4587	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4682837	0.82[JPT][hapmap]
rs4682844	0.82[JPT][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap]
rs4682845	0.93[ASN][1000 genomes]
rs4683296	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4683297	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4683298	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4683299	0.90[ASN][1000 genomes]
rs4683300	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683301	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442038	0.86[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6442039	0.85[ASN][1000 genomes]
rs6442040	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs6780601	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs724448	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724449	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724450	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7623898	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7628747	0.82[JPT][hapmap]
rs7635480	0.85[ASN][1000 genomes]
rs7645278	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7646906	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9852082	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9855938	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1138518	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs1138518	IMPDH2	cis	parietal	SCAN
rs1138518	CCDC12	cis	cerebellum	SCAN
rs1138518	SCAP	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46934400-46951000	Weak transcription	Psoas Muscle	Psoas
2	chr3:46934600-46949400	Weak transcription	Fetal Kidney	kidney
3	chr3:46939600-46945000	Weak transcription	K562	blood
4	chr3:46940400-46945000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:46940400-46950800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:46940600-46944800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:46940800-46945200	Weak transcription	Left Ventricle	heart
8	chr3:46940800-46950000	Weak transcription	Gastric	stomach
9	chr3:46941000-46944800	Weak transcription	HUVEC	blood vessel
10	chr3:46941000-46945000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:46941000-46949800	Weak transcription	Ovary	ovary
12	chr3:46941400-46944800	Weak transcription	Right Ventricle	heart
13	chr3:46941400-46945000	Weak transcription	HSMM	muscle
14	chr3:46941600-46944800	Weak transcription	Spleen	Spleen
15	chr3:46941800-46944800	Weak transcription	Placenta	Placenta
16	chr3:46941800-46944800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:46941800-46949200	Weak transcription	Adipose Nuclei	Adipose
18	chr3:46941800-46949600	Weak transcription	Fetal Lung	lung
19	chr3:46941800-46949600	Weak transcription	HSMMtube	muscle
20	chr3:46942000-46946000	Strong transcription	Fetal Stomach	stomach
21	chr3:46942000-46950600	Weak transcription	Fetal Intestine Small	intestine
22	chr3:46943000-46944400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:46944200-46944800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:46944200-46945000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:46944200-46950800	Weak transcription	Placenta Amnion	Placenta Amnion

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