Variant report

Variant	rs6768300
Chromosome Location	chr3:50649370-50649371
allele	C/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	RCOR1	chr3:50649248-50649650	Hela-S3	cervix:	n/a	n/a
2	HMGN3	chr3:50648830-50649900	K562	blood:	n/a	n/a
3	CREB1	chr3:50649005-50649516	A549	lung:	n/a	n/a
4	MAX	chr3:50648760-50649977	HepG2	liver:	n/a	chr3:50649698-50649708
5	CEBPB	chr3:50649230-50649681	Hela-S3	cervix:	n/a	n/a
6	TBL1XR1	chr3:50648836-50650647	K562	blood:	n/a	n/a
7	POLR2A	chr3:50648870-50649930	GM18951	blood:	n/a	n/a
8	REST	chr3:50648985-50649858	K562	blood:	n/a	chr3:50649329-50649347 chr3:50649263-50649276 chr3:50649263-50649276
9	POLR2A	chr3:50648950-50649416	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr3:50648882-50649566	SK-N-SH	brain:	n/a	n/a
11	RXRA	chr3:50649083-50649679	HepG2	liver:	n/a	n/a
12	STAT3	chr3:50649174-50649565	MCF10A-Er-Src	breast:	n/a	chr3:50649301-50649313 chr3:50649303-50649323 chr3:50649303-50649323 chr3:50649436-50649447 chr3:50649308-50649317 chr3:50649425-50649436 chr3:50649309-50649317 chr3:50649309-50649318
13	MYC	chr3:50649000-50649833	MCF10A-Er-Src	breast:	n/a	chr3:50649698-50649708
14	EP300	chr3:50649149-50649537	T-47D	breast:	n/a	n/a
15	NFYB	chr3:50649281-50650320	K562	blood:	n/a	chr3:50649464-50649479
16	GATA3	chr3:50648958-50650008	MCF-7	breast:	n/a	chr3:50649673-50649680 chr3:50649673-50649680 chr3:50649673-50649680
17	TAF1	chr3:50648870-50649413	K562	blood:	n/a	n/a
18	POLR2A	chr3:50648796-50650031	HUVEC	blood vessel:	n/a	n/a
19	CCNT2	chr3:50648070-50650438	K562	blood:	n/a	chr3:50650142-50650151
20	NFIC	chr3:50648832-50649947	ECC-1	luminal epithelium:	n/a	n/a
21	NFYA	chr3:50649280-50649782	Hela-S3	cervix:	n/a	chr3:50649467-50649485
22	PML	chr3:50648768-50649370	K562	blood:	n/a	n/a
23	GTF2F1	chr3:50648956-50649401	K562	blood:	n/a	n/a
24	MAX	chr3:50648680-50649930	A549	lung:	n/a	chr3:50649698-50649708
25	EP300	chr3:50649028-50649822	GM12878	blood:	n/a	n/a
26	ELF1	chr3:50649019-50649583	MCF-7	breast:	n/a	chr3:50649310-50649319
27	IRF1	chr3:50648779-50650474	K562	blood:	n/a	chr3:50649258-50649272
28	ETS1	chr3:50648879-50649496	K562	blood:	n/a	chr3:50649312-50649322 chr3:50649238-50649249
29	MAX	chr3:50648928-50649663	MCF-7	breast:	n/a	n/a
30	POLR2A	chr3:50648984-50649798	GM10847	blood:	n/a	n/a
31	MYC	chr3:50648921-50649418	HepG2	liver:	n/a	n/a
32	NFYB	chr3:50649255-50649766	Hela-S3	cervix:	n/a	chr3:50649464-50649479
33	POLR2A	chr3:50648715-50649857	H1-hESC	embryonic stem cell:	n/a	n/a
34	USF1	chr3:50649322-50649679	SK-N-SH_RA	brain:	n/a	n/a
35	MXI1	chr3:50648625-50650156	IMR90	lung:	n/a	n/a
36	POLR2A	chr3:50648916-50650007	HUVEC	blood vessel:	n/a	n/a
37	STAT1	chr3:50649054-50649648	GM12878	blood:	n/a	chr3:50649301-50649313 chr3:50649303-50649323 chr3:50649303-50649323 chr3:50649324-50649335 chr3:50649308-50649317 chr3:50649309-50649317 chr3:50649309-50649318
38	NR2F2	chr3:50649203-50650436	K562	blood:	n/a	n/a
39	RUNX3	chr3:50648874-50649910	GM12878	blood:	n/a	n/a
40	TBP	chr3:50648957-50649778	H1-hESC	embryonic stem cell:	n/a	n/a
41	MXI1	chr3:50648509-50650501	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr3:50648930-50649383	Hela-S3	cervix:	n/a	n/a
43	MAX	chr3:50648893-50650447	K562	blood:	n/a	chr3:50650147-50650157 chr3:50649698-50649708
44	NR2F2	chr3:50649085-50650596	K562	blood:	n/a	n/a
45	SIN3A	chr3:50648715-50649897	H1-hESC	embryonic stem cell:	n/a	chr3:50649338-50649349
46	POLR2A	chr3:50648909-50649415	U87	brain:	n/a	n/a
47	REST	chr3:50649065-50649440	K562	blood:	n/a	chr3:50649329-50649347 chr3:50649263-50649276 chr3:50649263-50649276
48	MAX	chr3:50648817-50649738	SK-N-SH	brain:	n/a	chr3:50649698-50649708
49	POLR2A	chr3:50648767-50649827	MCF-7	breast:	n/a	n/a
50	POLR2A	chr3:50646443-50650505	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39996045..39997746-chr3:50647710..50649775,2	MCF-7	breast:
2	chr3:50647669..50650476-chr3:51428019..51429805,2	K562	blood:
3	chr3:50613912..50618382-chr3:50647156..50650083,6	K562	blood:
4	chr3:50601756..50613871-chr3:50647072..50654542,28	K562	blood:
5	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
6	chr3:50648976..50652431-chr3:51425600..51429805,4	K562	blood:
7	chr3:50381829..50384513-chr3:50648626..50650726,2	MCF-7	breast:
8	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:
9	chr3:50649338..50651152-chr3:51428545..51430321,2	MCF-7	breast:
10	chr3:50649298..50656086-chr3:51426248..51430836,9	MCF-7	breast:
11	chr3:50648868..50649464-chr6:31670692..31671466,2	NB4	blood:
12	chr3:50606849..50607389-chr3:50649262..50649796,2	K562	blood:
13	chr3:50272604..50274758-chr3:50646990..50649583,2	K562	blood:

Variant related genes	Relation type
MAPKAPK3	TF binding region
CISH	TF binding region
ENSG00000004838	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000179837	Chromatin interaction
ENSG00000114735	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1034405	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130252	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11130255	0.81[EUR][1000 genomes]
rs11130263	0.83[AMR][1000 genomes]
rs11710858	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13075344	0.81[AMR][1000 genomes]
rs13076850	0.85[EUR][1000 genomes]
rs13083004	0.85[EUR][1000 genomes]
rs13084476	0.80[EUR][1000 genomes]
rs13084771	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13085096	0.81[AMR][1000 genomes]
rs13089719	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13091933	0.82[EUR][1000 genomes]
rs13094336	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13094785	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13096264	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13096772	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs175634	0.82[EUR][1000 genomes]
rs17787569	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs201194	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs201196	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs201197	0.80[AMR][1000 genomes]
rs201198	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2085580	0.83[AMR][1000 genomes]
rs2227280	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2232253	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2269507	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2355321	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2355705	0.83[AMR][1000 genomes]
rs34202063	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34266990	0.81[AMR][1000 genomes]
rs34390947	0.81[AMR][1000 genomes]
rs34399912	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34492910	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34584636	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34632971	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34756253	0.80[EUR][1000 genomes]
rs34846525	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34866096	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34889917	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35429015	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35531616	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35566897	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35655236	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35690191	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35714264	0.82[EUR][1000 genomes]
rs36011798	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3804628	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs399484	0.83[EUR][1000 genomes]
rs414171	0.90[EUR][1000 genomes]
rs4482663	0.83[AMR][1000 genomes]
rs490634	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59949730	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61549968	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs622502	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446210	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66867590	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67588094	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67813889	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6784166	0.82[EUR][1000 genomes]
rs6787521	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6791880	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68191286	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71326937	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71326944	0.81[EUR][1000 genomes]
rs73072418	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73072442	0.81[EUR][1000 genomes]
rs7611428	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7652715	0.83[AMR][1000 genomes]
rs809451	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830920	0.84[AMR][1000 genomes];0.83[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	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 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	chr3:50647200-50649800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:50647600-50650000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:50647600-50650000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:50647800-50649800	Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr3:50647800-50650200	Active TSS	Fetal Kidney	kidney
6	chr3:50648000-50650000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:50648000-50650200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr3:50648200-50649400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr3:50648200-50649600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr3:50648200-50649800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:50648200-50650000	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr3:50648200-50650000	Active TSS	Fetal Intestine Large	intestine
13	chr3:50648200-50650000	Active TSS	Small Intestine	intestine
14	chr3:50648400-50649800	Active TSS	Primary T cells from cord blood	blood
15	chr3:50648400-50649800	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr3:50648400-50649800	Active TSS	Gastric	stomach
17	chr3:50648400-50650000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:50648400-50650000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr3:50648400-50650000	Active TSS	Fetal Lung	lung
20	chr3:50648400-50650000	Active TSS	Placenta Amnion	Placenta Amnion
21	chr3:50648400-50650000	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr3:50648400-50650200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:50648400-50650200	Active TSS	Ovary	ovary
24	chr3:50648600-50649800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:50648600-50649800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr3:50648600-50649800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr3:50648600-50649800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:50648600-50649800	Active TSS	Duodenum Mucosa	Duodenum
29	chr3:50648600-50649800	Active TSS	Placenta	Placenta
30	chr3:50648600-50649800	Active TSS	Left Ventricle	heart
31	chr3:50648600-50649800	Active TSS	A549	lung
32	chr3:50648600-50650000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr3:50648600-50650000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:50648600-50650000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:50648600-50650000	Active TSS	Liver	Liver
36	chr3:50648600-50650000	Active TSS	HSMMtube	muscle
37	chr3:50648600-50650200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
38	chr3:50648600-50650200	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr3:50648600-50650200	Active TSS	Fetal Intestine Small	intestine
40	chr3:50648600-50650400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr3:50648600-50650400	Active TSS	Psoas Muscle	Psoas
42	chr3:50648600-50650400	Active TSS	K562	blood
43	chr3:50648800-50649600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:50648800-50649600	Active TSS	Thymus	Thymus
45	chr3:50648800-50649600	Active TSS	NHLF	lung
46	chr3:50648800-50649800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:50648800-50649800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:50648800-50649800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:50648800-50649800	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr3:50648800-50649800	Active TSS	Fetal Stomach	stomach

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