Variant report

Variant	rs12442297
Chromosome Location	chr15:44168470-44168471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:44168313-44168589	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr15:44168367-44168698	K562	blood:	n/a	n/a
3	POLR2A	chr15:44168265-44169072	SK-N-MC	brain:	n/a	n/a
4	TBP	chr15:44168440-44168639	K562	blood:	n/a	n/a
5	POLR2A	chr15:44168337-44168492	A549	lung:	n/a	n/a
6	POLR2A	chr15:44168212-44168593	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:44168330-44168481	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr15:44168122-44168673	K562	blood:	n/a	n/a
9	POLR2A	chr15:44168355-44168475	HepG2	liver:	n/a	n/a
10	POLR2A	chr15:44168291-44168493	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr15:44168298-44168706	K562	blood:	n/a	n/a
12	POLR2A	chr15:44168286-44168646	PFSK-1	brain:	n/a	n/a
13	HEY1	chr15:44168269-44168520	HepG2	liver:	n/a	n/a
14	POLR2A	chr15:44168124-44168472	MCF-7	breast:	n/a	n/a
15	POLR2A	chr15:44168290-44169432	K562	blood:	n/a	n/a
16	POLR2A	chr15:44168257-44168556	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr15:44168352-44168492	HepG2	liver:	n/a	n/a
18	HEY1	chr15:44168325-44168483	HepG2	liver:	n/a	n/a
19	POLR2A	chr15:44168292-44168607	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44168451..44168965-chrX:71401058..71401928,2	MCF-7	breast:
2	15:43782117-43785993..15:44168450-44170954	GM12878	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MFAP1-3	chr15:44168024-44170369	NONHSAT042137

No data

Variant related genes	Relation type
PIN4P1	TF binding region
ENSG00000067369	Chromatin interaction
ENSG00000102309	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10163054	0.88[CEU][hapmap];0.87[GIH][hapmap]
rs10438303	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs11070408	0.88[CEU][hapmap];0.87[GIH][hapmap]
rs11852767	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11856495	0.96[EUR][1000 genomes]
rs11856795	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12440573	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12441127	1.00[CEU][hapmap]
rs12441861	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs12441984	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12702	1.00[CEU][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.90[EUR][1000 genomes]
rs13329084	0.87[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16950562	1.00[CEU][hapmap]
rs16965120	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs16977724	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16977798	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1965794	0.92[EUR][1000 genomes]
rs1965795	0.89[EUR][1000 genomes]
rs2228368	0.90[EUR][1000 genomes]
rs2277531	1.00[CEU][hapmap]
rs2467402	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs2467426	0.88[CEU][hapmap]
rs2788	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs28413704	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28413881	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28437196	0.89[EUR][1000 genomes]
rs28476182	0.95[EUR][1000 genomes]
rs28509275	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs28513374	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28519630	0.96[EUR][1000 genomes]
rs28524541	0.96[EUR][1000 genomes]
rs28531819	0.96[EUR][1000 genomes]
rs28564774	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28583806	0.90[EUR][1000 genomes]
rs28590651	0.90[EUR][1000 genomes]
rs28636829	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs28674750	0.90[EUR][1000 genomes]
rs28679673	0.96[EUR][1000 genomes]
rs28684672	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs28687459	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28696802	0.96[EUR][1000 genomes]
rs28699233	0.87[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs28707214	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28780699	0.96[EUR][1000 genomes]
rs28781888	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28823973	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28858500	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28866846	0.96[EUR][1000 genomes]
rs2955969	0.81[CHB][hapmap]
rs3736180	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3742982	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3759790	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3759791	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs3784275	0.87[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs3816792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs3825783	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs3862142	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs4597285	0.89[EUR][1000 genomes]
rs472385	0.92[ASN][1000 genomes]
rs4997480	1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap]
rs56008017	0.90[EUR][1000 genomes]
rs56909447	0.93[EUR][1000 genomes]
rs61390361	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67541383	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68079546	0.96[EUR][1000 genomes]
rs7167976	0.90[GIH][hapmap]
rs7169322	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7169988	1.00[CEU][hapmap]
rs7170751	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7171750	1.00[CEU][hapmap]
rs7174208	1.00[CEU][hapmap]
rs7175032	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs7179388	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7181039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7183809	0.96[EUR][1000 genomes]
rs8023458	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs8023508	1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs8032649	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8033995	1.00[CEU][hapmap]
rs8040839	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9944216	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9989313	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12442297	ADAL	cis	Adipose Subcutaneous	GTEx
rs12442297	ADAL	cis	Esophagus Muscularis	GTEx
rs12442297	ADAL	cis	lung	GTEx
rs12442297	C15orf63	cis	lymphoblastoid	seeQTL
rs12442297	ADAL	cis	Artery Tibial	GTEx
rs12442297	ADAL	cis	Nerve Tibial	GTEx
rs12442297	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs12442297	ADAL	cis	Thyroid	GTEx
rs12442297	ELL3	cis	lymphoblastoid	seeQTL
rs12442297	SERF2	cis	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44119600-44169400	Weak transcription	Fetal Intestine Large	intestine
2	chr15:44119600-44172800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:44119600-44181800	Weak transcription	Small Intestine	intestine
4	chr15:44119600-44183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:44121000-44177600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:44144800-44181000	Weak transcription	HepG2	liver
7	chr15:44146800-44181600	Weak transcription	Gastric	stomach
8	chr15:44147600-44172000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:44150600-44174600	Strong transcription	Dnd41	blood
10	chr15:44151600-44171200	Weak transcription	Placenta	Placenta
11	chr15:44151600-44181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:44152000-44172800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:44152600-44168600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:44152600-44169600	Weak transcription	Lung	lung
15	chr15:44152600-44180800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:44153800-44172000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:44156800-44169600	Weak transcription	NHDF-Ad	bronchial
18	chr15:44156800-44206400	Weak transcription	Fetal Brain Male	brain
19	chr15:44157400-44172200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:44158200-44174000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:44158600-44169600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:44158600-44172800	Weak transcription	Primary B cells from cord blood	blood
23	chr15:44158600-44180800	Weak transcription	Fetal Lung	lung
24	chr15:44158800-44173200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr15:44159000-44170400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr15:44159000-44171800	Weak transcription	Adipose Nuclei	Adipose
27	chr15:44159000-44172800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:44160200-44172800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr15:44161400-44169400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:44161600-44172400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:44162200-44171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:44162200-44186000	Weak transcription	HSMM	muscle
33	chr15:44162400-44171600	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:44163000-44179400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:44163400-44177200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:44164000-44175400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr15:44164800-44176000	Weak transcription	K562	blood
38	chr15:44165000-44169400	Weak transcription	Primary T cells from cord blood	blood
39	chr15:44165000-44170400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:44165200-44174400	Strong transcription	Fetal Stomach	stomach
41	chr15:44165800-44172000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:44165800-44177200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:44166000-44184600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:44166400-44186600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:44166600-44168800	Weak transcription	Right Atrium	heart
46	chr15:44166600-44170000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:44166600-44171800	Weak transcription	Brain Angular Gyrus	brain
48	chr15:44166600-44172000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:44166600-44172600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:44166600-44182600	Weak transcription	HUVEC	blood vessel

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