Variant report

Variant	rs2166478
Chromosome Location	chr2:47084204-47084205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:47084194-47084244	Caco-2	colon:	n/a
2	chr2:47084194-47084244	HCT-116	colon:	n/a
3	chr2:47084194-47084244	CMK	blood:	n/a
4	chr2:47084194-47084244	GM06990	blood:	n/a
5	chr2:47084194-47084244	T-47D	breast:	n/a
6	chr2:47084194-47084244	PFSK-1	brain:	n/a
7	chr2:47084194-47084244	SKMC	muscle:	n/a
8	chr2:47084194-47084244	NH-A	brain:	n/a
9	chr2:47084194-47084244	HEEpiC	esophagus:	n/a
10	chr2:47084194-47084244	ProgFib	skin:	n/a
11	chr2:47084194-47084244	PANC-1	pancreas:	n/a
12	chr2:47084194-47084244	AG04449	skin:	fetal
13	chr2:47084194-47084244	NB4	blood:	n/a
14	chr2:47084194-47084244	A549	lung:	n/a
15	chr2:47084194-47084244	HL-60	blood:	n/a
16	chr2:47084194-47084244	Hepatocyte	liver:	n/a
17	chr2:47084194-47084244	RPTEC	kidney:	n/a
18	chr2:47084194-47084244	AG09319	gingival:	n/a
19	chr2:47084194-47084244	AoSMC	blood vessel:	n/a
20	chr2:47084194-47084244	HMEC	breast:	n/a
21	chr2:47084194-47084244	NT2-D1	testis:	n/a
22	chr2:47084194-47084244	SK-N-MC	brain:	n/a
23	chr2:47084194-47084244	ECC-1	luminal epithelium:	n/a
24	chr2:47084194-47084244	U87	brain:	n/a
25	chr2:47084194-47084244	HUVEC	blood vessel:	n/a
26	chr2:47084194-47084244	HNPCEpiC	eye:	n/a
27	chr2:47084194-47084244	HepG2	liver:	n/a
28	chr2:47084194-47084244	NHDF-neo	bronchial:	n/a
29	chr2:47084194-47084244	HEK293	kidney:	embryo
30	chr2:47084194-47084244	GM19239	blood:	n/a
31	chr2:47084194-47084244	SAEC	small airway:	n/a
32	chr2:47084194-47084244	Hela-S3	cervix:	n/a
33	chr2:47084194-47084244	Jurkat	blood:	n/a
34	chr2:47084194-47084244	AG04450	lung:	fetal
35	chr2:47084194-47084244	HRE	kidney:	n/a
36	chr2:47084194-47084244	HCM	heart:	n/a
37	chr2:47084194-47084244	MCF10A-Er-Src	breast:	n/a
38	chr2:47084194-47084244	HIPEpiC	eye:	n/a
39	chr2:47084194-47084244	GM12892	blood:	n/a
40	chr2:47084194-47084244	SK-N-SH_RA	brain:	n/a
41	chr2:47084194-47084244	MCF-7	breast:	n/a
42	chr2:47084194-47084244	BE2_C	brain:	n/a
43	chr2:47084194-47084244	ovcar-3	ovarian:	n/a
44	chr2:47084194-47084244	AG09309	skin:	n/a
45	chr2:47084194-47084244	AG10803	skin:	n/a
46	chr2:47084194-47084244	GM12891	blood:	n/a
47	chr2:47084194-47084244	NHBE	bronchial:	n/a
48	chr2:47084194-47084244	HCF	heart:	n/a
49	chr2:47084194-47084244	IMR90	lung:	fetal
50	chr2:47084194-47084244	BJ	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46926240..46928505-chr2:47083626..47085275,2	MCF-7	breast:
2	chr2:47081481..47084069-chr2:47084141..47086048,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226548	CpG island
ENSG00000171150	Chromatin interaction
ENSG00000239332	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10170987	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10177555	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10177751	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10183609	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11125096	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11125097	0.94[ASN][1000 genomes]
rs11686200	0.83[MEX][hapmap]
rs11687883	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11689551	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278711	0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4953433	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6759066	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9225	0.81[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs935372	0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs935379	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2166478	TTC7A	cis	cerebellum	SCAN
rs2166478	ATP6V1E2	cis	cerebellum	SCAN
rs2166478	ABCG8	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47075200-47084400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:47077200-47086200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:47078000-47085200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:47078000-47085200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:47080600-47085000	Weak transcription	K562	blood
6	chr2:47080800-47103600	Enhancers	Placenta	Placenta
7	chr2:47081200-47087200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:47081400-47086400	Enhancers	HMEC	breast
9	chr2:47081400-47086600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:47081400-47087200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:47081400-47087800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:47081400-47091000	Enhancers	NHDF-Ad	bronchial
13	chr2:47081600-47084400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:47081600-47084400	Enhancers	HSMM	muscle
15	chr2:47081600-47085600	Enhancers	NH-A	brain
16	chr2:47081600-47087800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr2:47082200-47085000	Weak transcription	Small Intestine	intestine
18	chr2:47082200-47085200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:47082200-47085200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:47082200-47085400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:47082200-47089000	Weak transcription	Colonic Mucosa	Colon
22	chr2:47082800-47084400	Enhancers	Stomach Smooth Muscle	stomach
23	chr2:47082800-47085000	Weak transcription	Fetal Lung	lung
24	chr2:47083000-47084400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:47083000-47086200	Weak transcription	Adipose Nuclei	Adipose
26	chr2:47083200-47088600	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:47083400-47084400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:47083400-47085000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:47083400-47086000	Enhancers	NHEK	skin
30	chr2:47083600-47085200	Weak transcription	Fetal Stomach	stomach
31	chr2:47083800-47085000	Weak transcription	Fetal Intestine Small	intestine
32	chr2:47083800-47085200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:47083800-47085200	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:47083800-47085200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:47083800-47085200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:47083800-47085200	Weak transcription	HSMMtube	muscle
37	chr2:47083800-47086200	Enhancers	A549	lung
38	chr2:47084000-47084600	Enhancers	Hela-S3	cervix
39	chr2:47084000-47085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:47084000-47085000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:47084000-47085000	Weak transcription	HUVEC	blood vessel
42	chr2:47084000-47086800	Weak transcription	Spleen	Spleen
43	chr2:47084000-47088400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:47084000-47088800	Weak transcription	Right Ventricle	heart
45	chr2:47084000-47093200	Weak transcription	Ovary	ovary
46	chr2:47084000-47093600	Weak transcription	Right Atrium	heart
47	chr2:47084200-47084600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:47084200-47085000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:47084200-47085000	Weak transcription	NHLF	lung
50	chr2:47084200-47085200	Weak transcription	Fetal Intestine Large	intestine

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