Variant report

Variant	rs3809125
Chromosome Location	chr12:56844349-56844350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56844086-56844454	HepG2	liver:	n/a	n/a
2	MXI1	chr12:56842301-56844522	SK-N-SH	brain:	n/a	chr12:56843229-56843238

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56844339-56844389	NB4	blood:	n/a
2	chr12:56844339-56844389	T-47D	breast:	n/a
3	chr12:56844339-56844389	AG09319	gingival:	n/a
4	chr12:56844339-56844389	PrEC	prostate:	n/a
5	chr12:56844339-56844389	Caco-2	colon:	n/a
6	chr12:56844339-56844389	A549	lung:	n/a
7	chr12:56844339-56844389	HepG2	liver:	n/a
8	chr12:56844339-56844389	Jurkat	blood:	n/a
9	chr12:56844339-56844389	MCF-7	breast:	n/a
10	chr12:56844339-56844389	PANC-1	pancreas:	n/a
11	chr12:56844339-56844389	AG09309	skin:	n/a
12	chr12:56844339-56844389	HUVEC	blood vessel:	n/a
13	chr12:56844339-56844389	ProgFib	skin:	n/a
14	chr12:56844339-56844389	HCT-116	colon:	n/a
15	chr12:56844339-56844389	K562	blood:	n/a
16	chr12:56844339-56844389	HRE	kidney:	n/a
17	chr12:56844339-56844389	Hepatocyte	liver:	n/a
18	chr12:56844339-56844389	SK-N-SH_RA	brain:	n/a
19	chr12:56844339-56844389	SKMC	muscle:	n/a
20	chr12:56844339-56844389	HEK293	kidney:	embryo
21	chr12:56844339-56844389	HCPEpiC	choroid plexus:	n/a
22	chr12:56844339-56844389	MCF10A-Er-Src	breast:	n/a
23	chr12:56844339-56844389	HRPEpiC	eye:	n/a
24	chr12:56844339-56844389	GM12878	blood:	n/a
25	chr12:56844339-56844389	SAEC	small airway:	n/a
26	chr12:56844339-56844389	NT2-D1	testis:	n/a
27	chr12:56844339-56844389	HCM	heart:	n/a
28	chr12:56844339-56844389	IMR90	lung:	fetal
29	chr12:56844339-56844389	ovcar-3	ovarian:	n/a
30	chr12:56844339-56844389	SK-N-SH	brain:	n/a
31	chr12:56844339-56844389	HIPEpiC	eye:	n/a
32	chr12:56844339-56844389	AoSMC	blood vessel:	n/a
33	chr12:56844339-56844389	LNCaP	prostate:	n/a
34	chr12:56844339-56844389	U87	brain:	n/a
35	chr12:56844339-56844389	HMEC	breast:	n/a
36	chr12:56844339-56844389	GM19239	blood:	n/a
37	chr12:56844339-56844389	AG10803	skin:	n/a
38	chr12:56844339-56844389	SK-N-MC	brain:	n/a
39	chr12:56844339-56844389	Hela-S3	cervix:	n/a
40	chr12:56844339-56844389	BJ	skin:	n/a
41	chr12:56844339-56844389	CMK	blood:	n/a
42	chr12:56844339-56844389	PFSK-1	brain:	n/a
43	chr12:56844339-56844389	RPTEC	kidney:	n/a
44	chr12:56844339-56844389	ECC-1	luminal epithelium:	n/a
45	chr12:56844339-56844389	HAEpiC	amniotic membrane:	n/a
46	chr12:56844339-56844389	HL-60	blood:	n/a
47	chr12:56844339-56844389	NHBE	bronchial:	n/a
48	chr12:56844339-56844389	BE2_C	brain:	n/a
49	chr12:56844339-56844389	HRCEpiC	kidney:	n/a
50	chr12:56844339-56844389	H1-hESC	embryonic stem cell:	embryo

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56841852..56845371-chr12:56847401..56851228,5	MCF-7	breast:
2	chr12:56751886..56753976-chr12:56841675..56844416,2	MCF-7	breast:
3	chr12:56660541..56662751-chr12:56842837..56845595,2	MCF-7	breast:
4	chr12:56823780..56826763-chr12:56843201..56845054,2	MCF-7	breast:
5	chr12:56839562..56844740-chr12:56860089..56866019,9	MCF-7	breast:
6	chr12:56843620..56845384-chr12:56856512..56859341,2	MCF-7	breast:
7	chr12:56684593..56687796-chr12:56843466..56846385,3	K562	blood:
8	chr12:56841673..56844476-chr12:56882161..56884243,2	MCF-7	breast:
9	chr12:56841526..56846188-chr12:56861608..56864760,4	K562	blood:
10	chr12:56510141..56512052-chr12:56841744..56844555,2	MCF-7	breast:
11	chr12:56726610..56729385-chr12:56842009..56844680,3	MCF-7	breast:
12	chr12:56726826..56730263-chr12:56843766..56846381,3	K562	blood:
13	chr12:56753916..56755760-chr12:56841528..56845904,3	K562	blood:

No data

Variant related genes	Relation type
TIMELESS	TF binding region
TIMELESS	CpG island
ENSG00000135423	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000176422	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10876889	0.83[ASN][1000 genomes]
rs10876890	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11171847	0.86[ASN][1000 genomes]
rs11171848	0.88[ASN][1000 genomes]
rs11171849	0.88[ASN][1000 genomes]
rs11171850	0.82[CEU][hapmap];0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs11171852	0.89[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11171856	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.97[ASN][1000 genomes]
rs11610921	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11833581	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs11833583	0.87[ASN][1000 genomes]
rs12299614	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs12313431	0.87[ASN][1000 genomes]
rs12316810	0.92[ASN][1000 genomes]
rs12815993	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1976294	0.80[ASN][1000 genomes]
rs2279665	0.82[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs2291738	0.81[ASW][hapmap];0.89[CEU][hapmap]
rs2371455	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638304	0.85[ASN][1000 genomes]
rs2657882	0.86[ASN][1000 genomes]
rs2657883	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2939303	0.94[ASN][1000 genomes]
rs34520497	0.86[ASN][1000 genomes]
rs34644700	0.88[ASN][1000 genomes]
rs35634983	0.84[ASN][1000 genomes]
rs3782237	0.86[ASN][1000 genomes]
rs6581094	0.86[ASN][1000 genomes]
rs6581095	0.86[ASN][1000 genomes]
rs67027355	0.86[ASN][1000 genomes]
rs703829	0.82[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[ASN][1000 genomes]
rs7312888	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[ASN][1000 genomes]
rs774026	0.86[ASN][1000 genomes]
rs774027	0.82[CEU][hapmap];0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs774031	0.86[ASN][1000 genomes]
rs774032	0.86[ASN][1000 genomes]
rs774033	0.82[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[ASN][1000 genomes]
rs774034	0.85[CEU][hapmap];0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs774035	0.82[CEU][hapmap];0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs774036	0.81[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs774037	0.86[ASN][1000 genomes]
rs774039	0.82[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[ASN][1000 genomes]
rs774047	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs7977477	0.82[CEU][hapmap];0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs812278	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3809125	AMHR2	cis	parietal	SCAN
rs3809125	TAC3	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56843600-56844600	Enhancers	HSMMtube	muscle
2	chr12:56843600-56844800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr12:56843600-56845200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:56843600-56845400	Enhancers	Fetal Thymus	thymus
5	chr12:56843600-56852800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:56843800-56844400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:56843800-56844400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:56843800-56844600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:56843800-56844600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr12:56843800-56844600	Enhancers	Fetal Muscle Leg	muscle
11	chr12:56843800-56844600	Enhancers	HepG2	liver
12	chr12:56843800-56844800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr12:56843800-56844800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr12:56843800-56844800	Enhancers	Primary T cells from cord blood	blood
15	chr12:56843800-56844800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:56843800-56845000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr12:56843800-56845000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr12:56843800-56845200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr12:56843800-56845200	Weak transcription	K562	blood
20	chr12:56843800-56845400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr12:56843800-56858000	Weak transcription	Brain Anterior Caudate	brain
22	chr12:56844000-56846200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:56844200-56844600	Weak transcription	Thymus	Thymus
24	chr12:56844200-56844800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:56844200-56845000	Enhancers	H9 Cell Line	embryonic stem cell
26	chr12:56844200-56845200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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