Variant report

Variant	rs6716121
Chromosome Location	chr2:55458836-55458837
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	POLR2A	chr2:55458744-55464800	K562	blood:	n/a	n/a
2	ELF1	chr2:55458669-55460096	A549	lung:	n/a	chr2:55459306-55459319
3	SRF	chr2:55458697-55459049	H1-hESC	embryonic stem cell:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
4	SMARCC1	chr2:55458745-55460606	Hela-S3	cervix:	n/a	chr2:55459487-55459496
5	POLR2A	chr2:55458747-55464848	U87	brain:	n/a	n/a
6	MTA3	chr2:55458589-55461547	GM12878	blood:	n/a	n/a
7	HCFC1	chr2:55458624-55460325	K562	blood:	n/a	n/a
8	ELF1	chr2:55458502-55460607	HCT-116	colon:	n/a	chr2:55459306-55459319
9	SRF	chr2:55458647-55459625	ECC-1	luminal epithelium:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
10	POLR2A	chr2:55458731-55465585	GM12891	blood:	n/a	n/a
11	MAX	chr2:55458583-55460929	A549	lung:	n/a	n/a
12	POLR2A	chr2:55458589-55462559	HCT-116	colon:	n/a	n/a
13	MAX	chr2:55458827-55460650	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr2:55458643-55463921	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr2:55458760-55464736	HepG2	liver:	n/a	n/a
17	MYBL2	chr2:55458767-55460463	HepG2	liver:	n/a	n/a
18	PML	chr2:55458826-55460285	K562	blood:	n/a	n/a
19	SRF	chr2:55458454-55460313	HCT-116	colon:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
20	ELF1	chr2:55458560-55460252	MCF-7	breast:	n/a	chr2:55459306-55459319
21	MBD4	chr2:55458795-55461839	HepG2	liver:	n/a	n/a
22	MYC	chr2:55458695-55458956	MCF10A-Er-Src	breast:	n/a	n/a
23	ELK1	chr2:55458622-55460326	K562	blood:	n/a	chr2:55459307-55459316 chr2:55459307-55459316
24	ELF1	chr2:55458636-55459961	A549	lung:	n/a	chr2:55459306-55459319
25	WRNIP1	chr2:55458788-55461008	GM12878	blood:	n/a	n/a
26	ELF1	chr2:55458616-55460290	HCT-116	colon:	n/a	chr2:55459306-55459319
27	SRF	chr2:55458751-55459054	GM12878	blood:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
28	MYBL2	chr2:55458596-55460585	HepG2	liver:	n/a	n/a
29	EP300	chr2:55458585-55459960	K562	blood:	n/a	chr2:55458752-55458766 chr2:55459308-55459315
30	TAF1	chr2:55458653-55460646	A549	lung:	n/a	n/a
31	ATF2	chr2:55458796-55460366	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr2:55458775-55464779	Hela-S3	cervix:	n/a	n/a
33	REST	chr2:55458597-55460470	A549	lung:	n/a	n/a
34	MYC	chr2:55458743-55460637	K562	blood:	n/a	n/a
35	REST	chr2:55458703-55460585	H1-neurons	neurons:	n/a	n/a
36	TAF1	chr2:55458673-55460245	ECC-1	luminal epithelium:	n/a	n/a
37	ETS1	chr2:55458736-55460644	A549	lung:	n/a	chr2:55459307-55459316 chr2:55459307-55459316 chr2:55458873-55458887 chr2:55459306-55459319 chr2:55459485-55459498 chr2:55459307-55459316 chr2:55459486-55459499 chr2:55459305-55459315 chr2:55459307-55459316 chr2:55459307-55459316 chr2:55459304-55459319 chr2:55458879-55458886 chr2:55459309-55459318
38	ELF1	chr2:55458631-55460117	MCF-7	breast:	n/a	chr2:55459306-55459319
39	ELK1	chr2:55458652-55459966	Hela-S3	cervix:	n/a	chr2:55459307-55459316 chr2:55459307-55459316
40	POLR2A	chr2:55458800-55464614	K562	blood:	n/a	n/a
41	SRF	chr2:55458789-55458945	GM12878	blood:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
42	RFX5	chr2:55458689-55460063	Hela-S3	cervix:	n/a	n/a
43	MXI1	chr2:55458719-55460467	H1-hESC	embryonic stem cell:	n/a	n/a
44	PML	chr2:55458701-55461227	GM12878	blood:	n/a	n/a
45	MXI1	chr2:55458504-55461434	SK-N-SH	brain:	n/a	n/a
46	ZNF143	chr2:55458830-55460087	K562	blood:	n/a	chr2:55459489-55459498 chr2:55459494-55459509 chr2:55459491-55459510 chr2:55459487-55459496 chr2:55459487-55459505
47	TBP	chr2:55458688-55460164	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr2:55458788-55461332	Hela-S3	cervix:	n/a	n/a
49	ELF1	chr2:55458653-55460013	K562	blood:	n/a	chr2:55459306-55459319
50	ELF1	chr2:55458660-55460012	HepG2	liver:	n/a	chr2:55459306-55459319

No.	Distal block	Cell Line	Cell type
1	chr2:55458112..55461105-chr2:55507986..55510921,3	MCF-7	breast:
2	chr2:54195792..54198215-chr2:55457941..55460893,2	K562	blood:
3	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
4	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
5	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
6	chr2:55458256..55461079-chr2:55494634..55496499,3	K562	blood:
7	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
8	chr2:55458156..55461118-chr2:55494163..55499368,6	MCF-7	breast:
9	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:

Variant related genes	Relation type
RPS27A	TF binding region
ENSG00000085760	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10172326	0.83[YRI][hapmap]
rs10209298	1.00[EUR][1000 genomes]
rs11679663	0.91[YRI][hapmap]
rs11886358	1.00[EUR][1000 genomes]
rs11887112	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11888119	1.00[MEX][hapmap]
rs11889466	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11890896	1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11894557	1.00[MEX][hapmap]
rs11896438	1.00[EUR][1000 genomes]
rs11899921	1.00[MEX][hapmap]
rs11902622	1.00[EUR][1000 genomes]
rs12621144	0.89[LWK][hapmap];0.96[YRI][hapmap]
rs13012766	0.89[LWK][hapmap];0.91[YRI][hapmap]
rs13013134	1.00[YRI][hapmap]
rs13019355	0.95[YRI][hapmap]
rs13399572	1.00[MEX][hapmap]
rs17046771	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046787	0.86[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972077	1.00[EUR][1000 genomes]
rs3935223	0.86[LWK][hapmap];0.92[YRI][hapmap]
rs55726603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55735105	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56219595	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56887573	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56902676	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57489147	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57517202	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58016152	1.00[EUR][1000 genomes]
rs58207828	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58485503	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59832517	0.82[AMR][1000 genomes]
rs60944260	1.00[EUR][1000 genomes]
rs61197615	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545474	0.87[YRI][hapmap]
rs6545478	0.91[YRI][hapmap]
rs6707902	0.80[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6714830	0.87[YRI][hapmap]
rs6721728	0.80[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6723598	0.96[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6724153	0.96[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6736539	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936831	1.00[EUR][1000 genomes]
rs73936834	1.00[EUR][1000 genomes]
rs73936837	1.00[EUR][1000 genomes]
rs73936845	1.00[EUR][1000 genomes]
rs73936947	1.00[EUR][1000 genomes]
rs73936949	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936959	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936964	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7596403	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7608709	0.86[AFR][1000 genomes];1.00[AMR][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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55456200-55459000	Weak transcription	Spleen	Spleen
2	chr2:55457000-55459000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:55457800-55460000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:55457800-55460400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:55457800-55460400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr2:55458000-55460200	Active TSS	A549	lung
7	chr2:55458000-55460400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:55458200-55460000	Active TSS	K562	blood
9	chr2:55458200-55460200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:55458200-55460400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:55458200-55460600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:55458200-55460800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:55458200-55460800	Active TSS	HMEC	breast
14	chr2:55458400-55459000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr2:55458400-55459000	Flanking Active TSS	Brain Angular Gyrus	brain
16	chr2:55458400-55459000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:55458400-55459000	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr2:55458400-55459000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr2:55458400-55459000	Flanking Active TSS	HUVEC	blood vessel
20	chr2:55458400-55459200	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr2:55458400-55459200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr2:55458400-55459200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr2:55458400-55459400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:55458400-55459400	Flanking Active TSS	Liver	Liver
25	chr2:55458400-55459800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr2:55458400-55460200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr2:55458400-55460200	Active TSS	Stomach Smooth Muscle	stomach
28	chr2:55458400-55460400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr2:55458400-55460400	Active TSS	H1 Cell Line	embryonic stem cell
30	chr2:55458400-55460400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:55458400-55460400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:55458400-55460600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr2:55458400-55460600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:55458400-55460600	Active TSS	Aorta	Aorta
35	chr2:55458400-55460600	Active TSS	Fetal Stomach	stomach
36	chr2:55458400-55460600	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr2:55458400-55460600	Active TSS	Right Atrium	heart
38	chr2:55458400-55460600	Active TSS	GM12878-XiMat	blood
39	chr2:55458400-55460600	Active TSS	HSMM	muscle
40	chr2:55458400-55460600	Active TSS	NH-A	brain
41	chr2:55458400-55460600	Active TSS	NHLF	lung
42	chr2:55458400-55460800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:55458400-55460800	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr2:55458400-55460800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:55458400-55460800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:55458400-55460800	Active TSS	Fetal Kidney	kidney
47	chr2:55458400-55460800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr2:55458400-55461400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:55458600-55459000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr2:55458600-55459000	Flanking Active TSS	Brain Cingulate Gyrus	brain

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