Variant report

Variant	rs2242446
Chromosome Location	chr16:55690425-55690426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr16:55689999-55690819	H1-hESC	embryonic stem cell:	n/a	chr16:55690339-55690352
2	EP300	chr16:55688161-55692249	SK-N-SH	brain:	n/a	chr16:55689705-55689718 chr16:55690020-55690029 chr16:55689885-55689894
3	MXI1	chr16:55690025-55690890	H1-hESC	embryonic stem cell:	n/a	n/a
4	MXI1	chr16:55688987-55697373	SK-N-SH	brain:	n/a	n/a
5	CTBP2	chr16:55689339-55690944	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr16:55690165-55690662	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr16:55689837-55690903	H1-hESC	embryonic stem cell:	n/a	chr16:55690094-55690109 chr16:55690416-55690430 chr16:55689846-55689861
8	CTCF	chr16:55689768-55690525	H1-hESC	embryonic stem cell:	n/a	chr16:55690339-55690352
9	RAD21	chr16:55689895-55690527	H1-hESC	embryonic stem cell:	n/a	chr16:55690342-55690354 chr16:55690248-55690260
10	ZNF143	chr16:55689946-55690905	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr16:55689894-55690964	H1-hESC	embryonic stem cell:	n/a	chr16:55690094-55690109 chr16:55690416-55690430
12	GABPA	chr16:55689953-55690483	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr16:55689844-55691015	H1-hESC	embryonic stem cell:	n/a	chr16:55690076-55690087
14	RAD21	chr16:55690002-55690656	H1-hESC	embryonic stem cell:	n/a	chr16:55690342-55690354 chr16:55690565-55690575 chr16:55690248-55690260
15	MAX	chr16:55689740-55691031	H1-hESC	embryonic stem cell:	n/a	chr16:55690076-55690087
16	SIN3A	chr16:55689191-55690750	H1-hESC	embryonic stem cell:	n/a	chr16:55689545-55689554 chr16:55689826-55689835 chr16:55690038-55690049

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:55690381-55690431	AG04449	skin:	fetal
2	chr16:55690381-55690431	NHDF-neo	bronchial:	n/a
3	chr16:55690381-55690431	HepG2	liver:	n/a
4	chr16:55690381-55690431	HRPEpiC	eye:	n/a
5	chr16:55690378-55690428	BJ	skin:	n/a
6	chr16:55690378-55690428	MCF10A-Er-Src	breast:	n/a
7	chr16:55690378-55690428	SKMC	muscle:	n/a
8	chr16:55690378-55690428	NB4	blood:	n/a
9	chr16:55690381-55690431	HUVEC	blood vessel:	n/a
10	chr16:55690378-55690428	HRPEpiC	eye:	n/a
11	chr16:55690378-55690428	SK-N-SH_RA	brain:	n/a
12	chr16:55690381-55690431	H1-hESC	embryonic stem cell:	embryo
13	chr16:55690378-55690428	HCT-116	colon:	n/a
14	chr16:55690378-55690428	GM19239	blood:	n/a
15	chr16:55690378-55690428	AG09309	skin:	n/a
16	chr16:55690378-55690428	HEK293	kidney:	embryo
17	chr16:55690381-55690431	IMR90	lung:	fetal
18	chr16:55690381-55690431	ovcar-3	ovarian:	n/a
19	chr16:55690378-55690428	HIPEpiC	eye:	n/a
20	chr16:55690378-55690428	LNCaP	prostate:	n/a
21	chr16:55690381-55690431	Jurkat	blood:	n/a
22	chr16:55690378-55690428	HEEpiC	esophagus:	n/a
23	chr16:55690381-55690431	HRCEpiC	kidney:	n/a
24	chr16:55690378-55690428	T-47D	breast:	n/a
25	chr16:55690378-55690428	IMR90	lung:	fetal
26	chr16:55690378-55690428	SK-N-MC	brain:	n/a
27	chr16:55690378-55690428	Hela-S3	cervix:	n/a
28	chr16:55690381-55690431	GM19239	blood:	n/a
29	chr16:55690378-55690428	HCM	heart:	n/a
30	chr16:55690381-55690431	MCF10A-Er-Src	breast:	n/a
31	chr16:55690378-55690428	Hepatocyte	liver:	n/a
32	chr16:55690381-55690431	HEK293	kidney:	embryo
33	chr16:55690381-55690431	Hela-S3	cervix:	n/a
34	chr16:55690378-55690428	ProgFib	skin:	n/a
35	chr16:55690381-55690431	AG10803	skin:	n/a
36	chr16:55690381-55690431	SAEC	small airway:	n/a
37	chr16:55690381-55690431	Caco-2	colon:	n/a
38	chr16:55690378-55690428	HepG2	liver:	n/a
39	chr16:55690378-55690428	HRE	kidney:	n/a
40	chr16:55690381-55690431	NH-A	brain:	n/a
41	chr16:55690381-55690431	CMK	blood:	n/a
42	chr16:55690381-55690431	MCF-7	breast:	n/a
43	chr16:55690378-55690428	Jurkat	blood:	n/a
44	chr16:55690378-55690428	GM12878	blood:	n/a
45	chr16:55690378-55690428	HMEC	breast:	n/a
46	chr16:55690381-55690431	GM12878	blood:	n/a
47	chr16:55690381-55690431	RPTEC	kidney:	n/a
48	chr16:55690381-55690431	SKMC	muscle:	n/a
49	chr16:55690381-55690431	BJ	skin:	n/a
50	chr16:55690378-55690428	NHBE	bronchial:	n/a

Variant related genes	Relation type
SLC6A2	TF binding region
SLC6A2	CpG island

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11076111	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13333066	0.91[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs1362620	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1362621	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17247999	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17307291	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2397771	0.99[ASN][1000 genomes]
rs28386840	0.97[EUR][1000 genomes]
rs28501300	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28665972	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28693487	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3760019	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3785147	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs747107	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][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	nsv906673	chr16:55631035-55798370	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv431501	chr16:55639454-55789570	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv517827	chr16:55656355-55698027	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2758426	chr16:55669396-55983590	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2758649	chr16:55669396-55983590	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2242446	CNGB1	cis	cerebellum	SCAN
rs2242446	SLC6A2	cis	Skin Sun Exposed Lower leg	GTEx
rs2242446	GNAO1	cis	parietal	SCAN
rs2242446	RPGRIP1L	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:55689200-55690600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
2	chr16:55689200-55691000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
3	chr16:55689200-55691000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:55689200-55691200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr16:55689200-55691200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr16:55689400-55690800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr16:55689400-55690800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr16:55689400-55690800	Bivalent/Poised TSS	Colonic Mucosa	Colon
9	chr16:55689400-55691000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr16:55689400-55691000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:55689400-55691000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr16:55689400-55691000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr16:55689400-55691000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr16:55689400-55691000	Bivalent Enhancer	Liver	Liver
15	chr16:55689400-55691000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr16:55689400-55691000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
17	chr16:55689400-55691000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
18	chr16:55689400-55691200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr16:55689400-55691200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr16:55689400-55691600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr16:55689600-55690600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr16:55689600-55690800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr16:55689600-55690800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr16:55689600-55690800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr16:55689600-55690800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
26	chr16:55689600-55690800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:55689600-55690800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
28	chr16:55689600-55690800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
29	chr16:55689600-55690800	Enhancers	Pancreas	Pancrea
30	chr16:55689600-55691000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr16:55689600-55691000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr16:55689800-55690600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
33	chr16:55689800-55690600	Active TSS	Right Atrium	heart
34	chr16:55689800-55690600	Active TSS	HepG2	liver
35	chr16:55689800-55690800	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr16:55690000-55690800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr16:55690000-55690800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
38	chr16:55690000-55690800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
39	chr16:55690000-55691000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr16:55690000-55691000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
41	chr16:55690200-55690600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr16:55690200-55690600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
43	chr16:55690200-55690600	Flanking Bivalent TSS/Enh	NHEK	skin
44	chr16:55690200-55690800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr16:55690200-55690800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
46	chr16:55690200-55690800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
47	chr16:55690200-55691000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
48	chr16:55690200-55691000	Bivalent Enhancer	Esophagus	oesophagus
49	chr16:55690200-55691000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
50	chr16:55690200-55691200	Flanking Bivalent TSS/Enh	Placenta	Placenta

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