Variant report

Variant	rs16888192
Chromosome Location	chr6:56732193-56732194
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	MAFK	chr6:56732054-56732254	Hela-S3	cervix:	n/a	n/a
2	NFIC	chr6:56731799-56732349	SK-N-SH	brain:	n/a	n/a
3	STAT3	chr6:56731937-56732273	MCF10A-Er-Src	breast:	n/a	n/a
4	FOSL1	chr6:56731811-56732393	HCT-116	colon:	n/a	n/a
5	E2F4	chr6:56732048-56732248	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr6:56731932-56732242	SK-N-SH_RA	brain:	n/a	n/a
7	EP300	chr6:56731761-56732503	SK-N-SH	brain:	n/a	chr6:56732294-56732303
8	CEBPB	chr6:56731937-56732287	Hela-S3	cervix:	n/a	n/a
9	PBX3	chr6:56731738-56732423	SK-N-SH	brain:	n/a	n/a
10	JUND	chr6:56731836-56732426	SK-N-SH	brain:	n/a	n/a
11	JUND	chr6:56731797-56732384	SK-N-SH	brain:	n/a	n/a
12	FOS	chr6:56731941-56732285	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr6:56731967-56732278	Hela-S3	cervix:	n/a	n/a
14	GATA3	chr6:56731733-56732549	SK-N-SH	brain:	n/a	chr6:56732295-56732305
15	TCF12	chr6:56731719-56732485	SK-N-SH	brain:	n/a	n/a
16	FOS	chr6:56731926-56732284	MCF10A-Er-Src	breast:	n/a	n/a
17	CEBPB	chr6:56731960-56732258	IMR90	lung:	n/a	n/a
18	EP300	chr6:56731963-56732314	Hela-S3	cervix:	n/a	chr6:56732294-56732303
19	JUND	chr6:56731903-56732259	Hela-S3	cervix:	n/a	n/a
20	STAT3	chr6:56732090-56732277	MCF10A-Er-Src	breast:	n/a	n/a
21	TEAD4	chr6:56731824-56732483	SK-N-SH	brain:	n/a	n/a
22	FOSL2	chr6:56731776-56732373	A549	lung:	n/a	n/a
23	STAT3	chr6:56731946-56732277	MCF10A-Er-Src	breast:	n/a	n/a
24	JUN	chr6:56731939-56732280	HUVEC	blood vessel:	n/a	n/a
25	PBX3	chr6:56731712-56732426	SK-N-SH	brain:	n/a	n/a
26	STAT3	chr6:56731772-56732261	MCF10A-Er-Src	breast:	n/a	n/a
27	EP300	chr6:56731891-56732260	SK-N-SH_RA	brain:	n/a	n/a
28	FOSL2	chr6:56731799-56732429	SK-N-SH	brain:	n/a	n/a
29	TCF12	chr6:56731707-56732520	SK-N-SH	brain:	n/a	n/a
30	FOS	chr6:56731927-56732284	MCF10A-Er-Src	breast:	n/a	n/a
31	RCOR1	chr6:56731921-56732250	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr6:56731805-56732374	SK-N-SH	brain:	n/a	n/a
33	GATA3	chr6:56731768-56732544	SK-N-SH	brain:	n/a	chr6:56732295-56732305
34	FOS	chr6:56731941-56732283	MCF10A-Er-Src	breast:	n/a	n/a
35	RXRA	chr6:56731784-56732436	SK-N-SH	brain:	n/a	n/a
36	FOS	chr6:56731906-56732297	HUVEC	blood vessel:	n/a	n/a
37	CEBPB	chr6:56731951-56732243	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56726286..56729119-chr6:56729880..56733046,4	MCF-7	breast:
2	chr6:56725702..56727982-chr6:56732126..56734324,2	K562	blood:

Variant related genes	Relation type
RPL17P26	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13190784	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs13195825	0.81[EUR][1000 genomes]
rs13198597	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs13199024	0.81[EUR][1000 genomes]
rs13203600	0.81[EUR][1000 genomes]
rs13205022	0.82[EUR][1000 genomes]
rs13207768	0.81[EUR][1000 genomes]
rs13209099	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs13214893	0.85[EUR][1000 genomes]
rs13215883	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs13216793	0.82[EUR][1000 genomes]
rs1610157	0.81[EUR][1000 genomes]
rs16888184	0.84[EUR][1000 genomes]
rs16888186	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16888189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17684941	0.84[EUR][1000 genomes]
rs17685045	0.81[EUR][1000 genomes]
rs17752213	0.85[EUR][1000 genomes]
rs1870638	0.93[CEU][hapmap]
rs1903332	0.80[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28360570	0.83[EUR][1000 genomes]
rs34083827	0.84[EUR][1000 genomes]
rs35080938	0.80[EUR][1000 genomes]
rs35242294	0.81[EUR][1000 genomes]
rs35440408	0.85[EUR][1000 genomes]
rs4587171	0.92[CHB][hapmap]
rs60563401	0.82[EUR][1000 genomes]
rs6905603	0.81[EUR][1000 genomes]
rs6905658	0.82[EUR][1000 genomes]
rs6910414	0.85[EUR][1000 genomes]
rs6914293	0.81[EUR][1000 genomes]
rs6918949	0.81[EUR][1000 genomes]
rs6925518	0.82[EUR][1000 genomes]
rs6926742	0.82[EUR][1000 genomes]
rs71564864	0.81[EUR][1000 genomes]
rs7744240	0.93[CEU][hapmap]
rs7744799	0.93[CEU][hapmap]
rs7758867	0.80[AMR][1000 genomes]
rs7761729	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56723000-56732600	Weak transcription	Small Intestine	intestine
2	chr6:56724200-56733800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:56725600-56734800	Enhancers	Hela-S3	cervix
4	chr6:56727200-56734600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:56727600-56734400	Enhancers	HMEC	breast
6	chr6:56727800-56734800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:56728000-56734800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:56728000-56735000	Enhancers	HSMM	muscle
9	chr6:56728000-56735000	Enhancers	NHDF-Ad	bronchial
10	chr6:56728200-56733800	Enhancers	HSMMtube	muscle
11	chr6:56728200-56733800	Enhancers	Osteobl	bone
12	chr6:56728800-56734800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:56729000-56733000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:56729200-56733000	Enhancers	A549	lung
15	chr6:56729600-56732200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr6:56730000-56732200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr6:56730000-56733000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:56730400-56732200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr6:56730400-56733800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:56730400-56740400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:56730600-56733000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:56730600-56733000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:56730600-56733000	Weak transcription	NHEK	skin
24	chr6:56730800-56733000	Enhancers	HUVEC	blood vessel
25	chr6:56731000-56732200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr6:56731000-56732400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:56731000-56732600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr6:56731000-56733200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:56731200-56732400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr6:56731600-56732600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:56731600-56733000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:56731600-56734600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:56731800-56732200	Enhancers	Fetal Stomach	stomach
34	chr6:56731800-56732400	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr6:56731800-56732600	Enhancers	Fetal Intestine Small	intestine
36	chr6:56731800-56734600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:56731800-56734800	Enhancers	NH-A	brain
38	chr6:56732000-56732200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr6:56732000-56732400	Weak transcription	GM12878-XiMat	blood
40	chr6:56732000-56733400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:56732000-56733400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:56732000-56733800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr6:56732000-56734800	Enhancers	NHLF	lung

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