Variant report

Variant	rs2242116
Chromosome Location	chr3:46941116-46941117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr3:46941094-46941835	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46935290..46938710-chr3:46938764..46942918,5	K562	blood:
2	chr3:46924894..46926955-chr3:46938452..46941314,2	K562	blood:
3	chr3:46940978..46942499-chr3:47420565..47422731,2	MCF-7	breast:
4	chr3:46939682..46941906-chr3:46942383..46946161,3	K562	blood:
5	chr3:46939682..46941423-chr3:46942383..46944944,2	K562	blood:
6	chr3:46858188..46860125-chr3:46939783..46942119,2	K562	blood:
7	chr3:46940802..46943210-chr3:46954167..46956344,2	K562	blood:

No data

Variant related genes	Relation type
PTH1R	TF binding region
ENSG00000260236	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000160801	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1001284	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10461018	0.82[JPT][hapmap]
rs10865943	0.92[ASN][1000 genomes]
rs11130110	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs11130111	0.81[JPT][hapmap]
rs1138518	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]
rs11705936	0.92[ASN][1000 genomes]
rs11719795	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1466275	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061197	0.82[JPT][hapmap]
rs2168443	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
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];0.94[ASN][1000 genomes]
rs4539969	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4587	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4682837	0.82[JPT][hapmap]
rs4682844	0.82[JPT][hapmap]
rs4682845	0.93[ASN][1000 genomes]
rs4683296	0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4683297	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];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	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683301	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442038	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs6442039	0.85[ASN][1000 genomes]
rs6442040	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6780601	0.94[ASN][1000 genomes]
rs724448	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724449	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724450	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs7623898	0.94[ASN][1000 genomes]
rs7628747	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs7635480	0.85[ASN][1000 genomes]
rs7645278	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.94[ASN][1000 genomes]
rs7646906	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9852082	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9855938	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	esv3357520	chr3:46939998-46942796	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2242116	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs2242116	IMPDH2	cis	parietal	SCAN
rs2242116	SCAP	cis	parietal	SCAN
rs2242116	CCDC12	cis	cerebellum	SCAN

Chromatin state (count:38 , 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	chr3:46939400-46941400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
4	chr3:46939400-46941600	Enhancers	Spleen	Spleen
5	chr3:46939600-46941400	Bivalent Enhancer	Fetal Stomach	stomach
6	chr3:46939600-46941800	Enhancers	Fetal Lung	lung
7	chr3:46939600-46945000	Weak transcription	K562	blood
8	chr3:46940000-46941600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:46940000-46941800	Enhancers	Right Atrium	heart
10	chr3:46940200-46941200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
11	chr3:46940200-46941200	Flanking Active TSS	HSMM	muscle
12	chr3:46940400-46941800	Enhancers	Brain Substantia Nigra	brain
13	chr3:46940400-46942000	Enhancers	Brain Angular Gyrus	brain
14	chr3:46940400-46942000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:46940400-46942000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:46940400-46942000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:46940400-46945000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:46940400-46950800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:46940600-46941400	Enhancers	Brain Germinal Matrix	brain
20	chr3:46940600-46941400	Enhancers	Right Ventricle	heart
21	chr3:46940600-46941800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:46940600-46942000	Enhancers	Brain Anterior Caudate	brain
23	chr3:46940600-46942000	Enhancers	Brain Cingulate Gyrus	brain
24	chr3:46940600-46942000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:46940600-46942200	Enhancers	Brain Hippocampus Middle	brain
26	chr3:46940600-46943000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:46940600-46944800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:46940800-46941200	Flanking Active TSS	HSMMtube	muscle
29	chr3:46940800-46941400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:46940800-46941800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:46940800-46943800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr3:46940800-46945200	Weak transcription	Left Ventricle	heart
33	chr3:46940800-46950000	Weak transcription	Gastric	stomach
34	chr3:46941000-46941800	Enhancers	Adipose Nuclei	Adipose
35	chr3:46941000-46942200	Enhancers	Fetal Muscle Leg	muscle
36	chr3:46941000-46944800	Weak transcription	HUVEC	blood vessel
37	chr3:46941000-46945000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:46941000-46949800	Weak transcription	Ovary	ovary

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