Variant report

Variant	rs12039683
Chromosome Location	chr1:211590326-211590327
allele	A/G
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	E2F6	chr1:211590048-211590435	H1-hESC	embryonic stem cell:	n/a	chr1:211590286-211590295
2	MAX	chr1:211590166-211590608	Hela-S3	cervix:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
3	MYC	chr1:211590289-211590777	MCF10A-Er-Src	breast:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
4	POLR2A	chr1:211590322-211590526	Hela-S3	cervix:	n/a	n/a
5	RAD21	chr1:211590088-211590332	HepG2	liver:	n/a	chr1:211590289-211590301
6	TAF1	chr1:211589551-211590383	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:211590001-211590351	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr1:211589710-211590402	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:211590165-211590346	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:211589535-211590698	GM12892	blood:	n/a	n/a
11	BHLHE40	chr1:211590267-211590632	GM12878	blood:	n/a	n/a
12	TAF1	chr1:211589561-211590333	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:211589693-211590651	HepG2	liver:	n/a	n/a
14	MAX	chr1:211589997-211590482	H1-hESC	embryonic stem cell:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
15	USF1	chr1:211590326-211590644	A549	lung:	n/a	chr1:211590516-211590527
16	TBP	chr1:211589619-211590367	H1-hESC	embryonic stem cell:	n/a	n/a
17	MYC	chr1:211590215-211590664	MCF10A-Er-Src	breast:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
18	CTCF	chr1:211590111-211590327	HepG2	liver:	n/a	chr1:211590254-211590267 chr1:211590182-211590195 chr1:211590251-211590264
19	YY1	chr1:211589607-211590409	HepG2	liver:	n/a	chr1:211590286-211590295
20	MAX	chr1:211590096-211590473	ECC-1	luminal epithelium:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
21	POLR2A	chr1:211589431-211590586	ProgFib	skin:	n/a	n/a
22	HA-E2F1	chr1:211589507-211590489	MCF-7	breast:	n/a	chr1:211590286-211590295 chr1:211589820-211589829
23	MAZ	chr1:211589501-211590470	IMR90	lung:	n/a	chr1:211589803-211589813 chr1:211590325-211590334
24	MAX	chr1:211590099-211590396	H1-hESC	embryonic stem cell:	n/a	chr1:211590325-211590334
25	POLR2A	chr1:211589461-211590384	MCF-7	breast:	n/a	n/a
26	POLR2A	chr1:211590065-211590493	IMR90	lung:	n/a	n/a
27	POLR2A	chr1:211590083-211590621	PFSK-1	brain:	n/a	n/a
28	EBF1	chr1:211590162-211590472	GM12878	blood:	n/a	chr1:211590293-211590304
29	HDAC2	chr1:211590107-211590387	HepG2	liver:	n/a	n/a
30	FOS	chr1:211590290-211590639	HUVEC	blood vessel:	n/a	chr1:211590326-211590334 chr1:211590324-211590336
31	MAX	chr1:211589813-211590492	HepG2	liver:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
32	MYC	chr1:211590214-211590367	HepG2	liver:	n/a	chr1:211590325-211590334
33	CTCF	chr1:211590055-211590361	H1-hESC	embryonic stem cell:	n/a	chr1:211590254-211590267 chr1:211590182-211590195 chr1:211590251-211590264
34	MYC	chr1:211590323-211590595	HUVEC	blood vessel:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
35	ZNF143	chr1:211590151-211590341	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:211589419-211590420	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr1:211589998-211590474	ECC-1	luminal epithelium:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
38	POLR2A	chr1:211589503-211590370	MCF-7	breast:	n/a	n/a
39	POLR2A	chr1:211589558-211590522	A549	lung:	n/a	n/a
40	TAF1	chr1:211589553-211590422	H1-hESC	embryonic stem cell:	n/a	n/a
41	POU2F2	chr1:211590302-211590667	GM12878	blood:	n/a	n/a
42	RAD21	chr1:211589469-211590450	H1-hESC	embryonic stem cell:	n/a	chr1:211590289-211590301 chr1:211589686-211589700
43	GTF2F1	chr1:211590152-211590385	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr1:211590141-211590341	H1-hESC	embryonic stem cell:	n/a	chr1:211590289-211590301
45	MYC	chr1:211589999-211590340	MCF-7	breast:	n/a	chr1:211590325-211590334
46	USF1	chr1:211590261-211590712	A549	lung:	n/a	chr1:211590516-211590527
47	MAX	chr1:211590170-211590628	NB4	blood:	n/a	chr1:211590325-211590334 chr1:211590461-211590471
48	MXI1	chr1:211589961-211590809	IMR90	lung:	n/a	n/a
49	STAT3	chr1:211590320-211590643	MCF10A-Er-Src	breast:	n/a	chr1:211590479-211590490
50	E2F6	chr1:211590098-211590485	H1-hESC	embryonic stem cell:	n/a	chr1:211590286-211590295

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:211590292-211590342	PrEC	prostate:	n/a
2	chr1:211590292-211590342	MCF10A-Er-Src	breast:	n/a
3	chr1:211590292-211590342	SKMC	muscle:	n/a
4	chr1:211590292-211590342	AG04450	lung:	fetal
5	chr1:211590292-211590342	AG04449	skin:	fetal
6	chr1:211590292-211590342	Hela-S3	cervix:	n/a
7	chr1:211590292-211590342	HRPEpiC	eye:	n/a
8	chr1:211590292-211590342	AG09309	skin:	n/a
9	chr1:211590292-211590342	SAEC	small airway:	n/a
10	chr1:211590292-211590342	HCT-116	colon:	n/a
11	chr1:211590292-211590342	HRCEpiC	kidney:	n/a
12	chr1:211590292-211590342	GM06990	blood:	n/a
13	chr1:211590292-211590342	SK-N-MC	brain:	n/a
14	chr1:211590292-211590342	NT2-D1	testis:	n/a
15	chr1:211590292-211590342	NHBE	bronchial:	n/a
16	chr1:211590292-211590342	AG10803	skin:	n/a
17	chr1:211590292-211590342	H1-hESC	embryonic stem cell:	embryo
18	chr1:211590292-211590342	HMEC	breast:	n/a
19	chr1:211590292-211590342	NHDF-neo	bronchial:	n/a
20	chr1:211590292-211590342	HEEpiC	esophagus:	n/a
21	chr1:211590292-211590342	K562	blood:	n/a
22	chr1:211590292-211590342	SK-N-SH_RA	brain:	n/a
23	chr1:211590292-211590342	HAEpiC	amniotic membrane:	n/a
24	chr1:211590292-211590342	LNCaP	prostate:	n/a
25	chr1:211590292-211590342	NB4	blood:	n/a
26	chr1:211590292-211590342	SK-N-SH	brain:	n/a
27	chr1:211590292-211590342	HCF	heart:	n/a
28	chr1:211590292-211590342	BJ	skin:	n/a
29	chr1:211590292-211590342	ECC-1	luminal epithelium:	n/a
30	chr1:211590292-211590342	HL-60	blood:	n/a
31	chr1:211590292-211590342	Jurkat	blood:	n/a
32	chr1:211590292-211590342	HPAEpiC	pulmonary alveolar:	n/a
33	chr1:211590292-211590342	HCM	heart:	n/a
34	chr1:211590292-211590342	RPTEC	kidney:	n/a
35	chr1:211590292-211590342	T-47D	breast:	n/a
36	chr1:211590292-211590342	CMK	blood:	n/a
37	chr1:211590292-211590342	MCF-7	breast:	n/a
38	chr1:211590292-211590342	HIPEpiC	eye:	n/a
39	chr1:211590292-211590342	U87	brain:	n/a
40	chr1:211590292-211590342	BE2_C	brain:	n/a
41	chr1:211590292-211590342	NH-A	brain:	n/a
42	chr1:211590292-211590342	HCPEpiC	choroid plexus:	n/a
43	chr1:211590292-211590342	A549	lung:	n/a
44	chr1:211590292-211590342	AG09319	gingival:	n/a
45	chr1:211590292-211590342	Hepatocyte	liver:	n/a
46	chr1:211590292-211590342	GM12878	blood:	n/a
47	chr1:211590292-211590342	PANC-1	pancreas:	n/a
48	chr1:211590292-211590342	PFSK-1	brain:	n/a
49	chr1:211590292-211590342	AoSMC	blood vessel:	n/a
50	chr1:211590292-211590342	ProgFib	skin:	n/a

Variant related genes	Relation type
SNX25P1	TF binding region
SNX25P1	CpG island

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10458470	1.00[CEU][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10494935	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs10863885	1.00[CEU][hapmap]
rs11119717	1.00[CEU][hapmap]
rs11119720	1.00[CEU][hapmap]
rs11119725	1.00[CEU][hapmap]
rs11119730	1.00[MKK][hapmap]
rs11119731	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119733	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119734	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119737	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119738	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119740	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12027277	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12028306	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12030854	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12032988	0.92[EUR][1000 genomes]
rs12033418	0.85[AMR][1000 genomes]
rs12035966	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12039915	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12065190	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12080561	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12085730	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs12097572	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17017360	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17017401	1.00[CEU][hapmap]
rs2175633	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs2289758	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3738201	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738202	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4951521	1.00[CEU][hapmap]
rs57093875	0.89[ASN][1000 genomes]
rs58164259	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58510761	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60169087	0.85[AMR][1000 genomes]
rs61624054	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663729	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs6698113	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs6698191	1.00[CEU][hapmap];0.80[JPT][hapmap]

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	esv2762141	chr1:211538685-211603843	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	esv1824154	chr1:211565640-211614280	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
3	esv3362349	chr1:211588754-211591702	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	esv3433824	chr1:211589079-211591127	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211581400-211608200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:211581800-211590600	Weak transcription	Fetal Intestine Small	intestine
3	chr1:211585400-211593200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:211589200-211590400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:211589200-211590400	Enhancers	Primary B cells from cord blood	blood
6	chr1:211589200-211590400	Active TSS	Muscle Satellite Cultured Cells	--
7	chr1:211589200-211590400	Active TSS	Adipose Nuclei	Adipose
8	chr1:211589200-211590400	Active TSS	Duodenum Mucosa	Duodenum
9	chr1:211589200-211590400	Active TSS	NH-A	brain
10	chr1:211589200-211590600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:211589200-211590800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:211589400-211590400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:211589400-211590400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:211589400-211590400	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr1:211589400-211590400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr1:211589400-211590400	Active TSS	Primary T cells from cord blood	blood
17	chr1:211589400-211590400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:211589400-211590400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:211589400-211590400	Active TSS	Brain Anterior Caudate	brain
20	chr1:211589400-211590400	Active TSS	Brain Germinal Matrix	brain
21	chr1:211589400-211590400	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr1:211589400-211590400	Active TSS	Psoas Muscle	Psoas
23	chr1:211589400-211590400	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr1:211589400-211590400	Active TSS	HepG2	liver
25	chr1:211589400-211590400	Active TSS	HSMM	muscle
26	chr1:211589400-211590400	Active TSS	HUVEC	blood vessel
27	chr1:211589400-211590400	Active TSS	NHEK	skin
28	chr1:211589400-211590400	Active TSS	Osteobl	bone
29	chr1:211589400-211590600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:211589400-211590600	Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr1:211589400-211590600	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr1:211589400-211590600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:211589400-211590600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:211589400-211590600	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr1:211589400-211590600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr1:211589400-211590600	Active TSS	A549	lung
37	chr1:211589400-211590600	Active TSS	NHDF-Ad	bronchial
38	chr1:211589400-211591000	Active TSS	Brain Hippocampus Middle	brain
39	chr1:211589600-211590400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr1:211589600-211590400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:211589600-211590400	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:211589600-211590400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:211589600-211590400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:211589600-211590400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:211589600-211590400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:211589600-211590400	Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr1:211589600-211590400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr1:211589600-211590400	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr1:211589600-211590400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:211589600-211590400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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