Variant report

Variant	rs12209322
Chromosome Location	chr6:2437165-2437166
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:2437145-2437188	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:2437100-2437224	MCF-7	breast:	n/a	n/a
3	POLR2A	chr6:2437108-2437225	MCF-7	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:2437142-2437192	AG09319	gingival:	n/a
2	chr6:2437142-2437192	SK-N-SH_RA	brain:	n/a
3	chr6:2437142-2437192	HRE	kidney:	n/a
4	chr6:2437142-2437192	GM12891	blood:	n/a
5	chr6:2437147-2437197	Hepatocyte	liver:	n/a
6	chr6:2437142-2437192	ECC-1	luminal epithelium:	n/a
7	chr6:2437142-2437192	MCF10A-Er-Src	breast:	n/a
8	chr6:2437147-2437197	NH-A	brain:	n/a
9	chr6:2437142-2437192	MCF-7	breast:	n/a
10	chr6:2437147-2437197	SKMC	muscle:	n/a
11	chr6:2437147-2437197	HNPCEpiC	eye:	n/a
12	chr6:2437147-2437197	HAEpiC	amniotic membrane:	n/a
13	chr6:2437142-2437192	HUVEC	blood vessel:	n/a
14	chr6:2437147-2437197	NB4	blood:	n/a
15	chr6:2437147-2437197	AG04450	lung:	fetal
16	chr6:2437147-2437197	AG09309	skin:	n/a
17	chr6:2437142-2437192	BE2_C	brain:	n/a
18	chr6:2437147-2437197	NT2-D1	testis:	n/a
19	chr6:2437142-2437192	HIPEpiC	eye:	n/a
20	chr6:2437147-2437197	GM12891	blood:	n/a
21	chr6:2437142-2437192	AG04450	lung:	fetal
22	chr6:2437142-2437192	PANC-1	pancreas:	n/a
23	chr6:2437142-2437192	AG09309	skin:	n/a
24	chr6:2437142-2437192	RPTEC	kidney:	n/a
25	chr6:2437147-2437197	SK-N-SH	brain:	n/a
26	chr6:2437142-2437192	SK-N-SH	brain:	n/a
27	chr6:2437147-2437197	HEK293	kidney:	embryo
28	chr6:2437142-2437192	GM12878	blood:	n/a
29	chr6:2437147-2437197	BJ	skin:	n/a
30	chr6:2437147-2437197	CMK	blood:	n/a
31	chr6:2437142-2437192	GM19239	blood:	n/a
32	chr6:2437142-2437192	AG10803	skin:	n/a
33	chr6:2437142-2437192	HCF	heart:	n/a
34	chr6:2437147-2437197	SAEC	small airway:	n/a
35	chr6:2437147-2437197	NHDF-neo	bronchial:	n/a
36	chr6:2437142-2437192	ProgFib	skin:	n/a
37	chr6:2437147-2437197	Caco-2	colon:	n/a
38	chr6:2437147-2437197	U87	brain:	n/a
39	chr6:2437147-2437197	AG04449	skin:	fetal
40	chr6:2437147-2437197	MCF-7	breast:	n/a
41	chr6:2437147-2437197	SK-N-MC	brain:	n/a
42	chr6:2437147-2437197	HCPEpiC	choroid plexus:	n/a
43	chr6:2437147-2437197	HMEC	breast:	n/a
44	chr6:2437142-2437192	H1-hESC	embryonic stem cell:	embryo
45	chr6:2437142-2437192	PFSK-1	brain:	n/a
46	chr6:2437147-2437197	HepG2	liver:	n/a
47	chr6:2437142-2437192	HAEpiC	amniotic membrane:	n/a
48	chr6:2437142-2437192	Jurkat	blood:	n/a
49	chr6:2437147-2437197	AG09319	gingival:	n/a
50	chr6:2437142-2437192	GM12892	blood:	n/a

No data

Variant related genes	Relation type
ENSG00000272465	TF binding region
ENSG00000272465	CpG island

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10458063	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10458138	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10458139	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10458140	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10458141	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10458142	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11242766	0.81[EUR][1000 genomes]
rs11242769	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11242770	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11242772	0.90[CHD][hapmap];0.85[GIH][hapmap];0.85[EUR][1000 genomes]
rs11753825	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11758482	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12189681	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12189724	0.83[AMR][1000 genomes]
rs12195877	0.83[AMR][1000 genomes]
rs12196223	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12199363	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12199637	0.81[AMR][1000 genomes]
rs12205452	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12206851	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209220	0.83[AMR][1000 genomes]
rs12209326	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210286	0.82[AMR][1000 genomes]
rs12210452	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12213643	0.81[AMR][1000 genomes]
rs12528202	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12662045	0.80[AMR][1000 genomes]
rs13214014	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13214565	0.81[AMR][1000 genomes]
rs13220392	0.83[AMR][1000 genomes]
rs2073003	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076470	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294659	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34885387	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35144026	0.83[AMR][1000 genomes]
rs3734506	0.83[AMR][1000 genomes]
rs3817904	0.81[CHB][hapmap];0.83[CHD][hapmap];0.80[MEX][hapmap];0.83[AMR][1000 genomes]
rs9328099	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs982096	0.82[EUR][1000 genomes]
rs983027	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs983028	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription 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	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2399800-2449200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:2402200-2449200	Weak transcription	Left Ventricle	heart
3	chr6:2414600-2452000	Weak transcription	Ovary	ovary
4	chr6:2414800-2448800	Weak transcription	Liver	Liver
5	chr6:2414800-2449200	Weak transcription	Fetal Stomach	stomach
6	chr6:2417600-2454200	Weak transcription	Pancreas	Pancrea
7	chr6:2426400-2439800	Weak transcription	Aorta	Aorta
8	chr6:2428800-2446200	Weak transcription	Right Ventricle	heart
9	chr6:2431600-2439800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:2432200-2449200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:2433200-2449200	Weak transcription	Adipose Nuclei	Adipose
12	chr6:2433400-2437200	Weak transcription	HSMM	muscle
13	chr6:2433600-2447000	Weak transcription	Fetal Intestine Large	intestine
14	chr6:2434000-2437600	Enhancers	Fetal Kidney	kidney
15	chr6:2434000-2448400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:2434200-2442600	Weak transcription	Lung	lung
17	chr6:2434400-2449200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:2434600-2439800	Weak transcription	Spleen	Spleen
19	chr6:2435000-2449200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:2435400-2442000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:2435400-2449200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:2436200-2447000	Weak transcription	Fetal Intestine Small	intestine
23	chr6:2436400-2437200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:2437000-2437400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:2437000-2442000	Weak transcription	Placenta	Placenta

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