Variant report

Variant	rs56405707
Chromosome Location	chr6:27640246-27640247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27638059..27640499-chr6:27771985..27774359,2	MCF-7	breast:
2	chr6:27635682..27638550-chr6:27638732..27640689,2	K562	blood:
3	chr6:27521716..27523597-chr6:27638518..27641412,2	K562	blood:
4	chr6:27514797..27517693-chr6:27638878..27641841,2	K562	blood:
5	chr6:27638628..27643322-chr6:27645901..27648389,5	K562	blood:
6	chr6:27640023..27641609-chr6:27744727..27746412,2	K562	blood:
7	chr6:27638960..27640741-chr6:27721974..27723507,2	K562	blood:
8	chr6:27635489..27641593-chr6:27648456..27655439,10	K562	blood:
9	chr6:27638340..27640249-chr6:27659440..27661461,2	K562	blood:
10	chr6:27638297..27640693-chr6:27651718..27653720,2	MCF-7	breast:

No data

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10484399	0.87[EUR][1000 genomes]
rs13192965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193480	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13193542	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13194781	0.83[EUR][1000 genomes]
rs13195636	0.85[EUR][1000 genomes]
rs13195728	0.87[EUR][1000 genomes]
rs13199772	0.83[EUR][1000 genomes]
rs13199906	0.83[EUR][1000 genomes]
rs13202291	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13202295	0.94[EUR][1000 genomes]
rs13202775	0.92[EUR][1000 genomes]
rs13209332	0.85[EUR][1000 genomes]
rs13210634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13212318	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13212651	0.83[EUR][1000 genomes]
rs13215275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13217620	1.00[EUR][1000 genomes]
rs17695758	0.83[EUR][1000 genomes]
rs17749927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17750747	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17751184	0.87[EUR][1000 genomes]
rs17763089	0.83[EUR][1000 genomes]
rs34064842	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34105070	0.92[EUR][1000 genomes]
rs34194357	0.83[EUR][1000 genomes]
rs34409918	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34432857	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34573979	0.81[EUR][1000 genomes]
rs34706883	0.87[EUR][1000 genomes]
rs34718920	0.87[EUR][1000 genomes]
rs34965299	0.85[EUR][1000 genomes]
rs35037868	0.94[EUR][1000 genomes]
rs35501037	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35715914	1.00[EUR][1000 genomes]
rs35819751	0.83[EUR][1000 genomes]
rs35848276	0.85[EUR][1000 genomes]
rs36116761	0.83[EUR][1000 genomes]
rs45509595	0.83[EUR][1000 genomes]
rs58616630	0.81[EUR][1000 genomes]
rs66785117	0.85[EUR][1000 genomes]
rs67101035	0.87[EUR][1000 genomes]
rs67652222	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs71559038	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71559050	0.87[EUR][1000 genomes]
rs72845046	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs72845070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847313	1.00[AMR][1000 genomes];0.94[EUR][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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv525669	chr6:27623511-27657647	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv883511	chr6:27623511-27660508	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	esv2830157	chr6:27634640-27657647	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv518945	chr6:27634640-27668013	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56405707	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs56405707	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs56405707	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27634600-27640800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:27634800-27641400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:27635200-27641200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:27637800-27640600	Active TSS	Ovary	ovary
5	chr6:27638000-27640400	Weak transcription	Right Atrium	heart
6	chr6:27638000-27640600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:27638000-27640800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:27638000-27641200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:27638000-27641200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:27638000-27641400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr6:27638200-27641400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr6:27638400-27640400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:27638400-27641200	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr6:27638400-27641400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:27638400-27641400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr6:27638600-27641000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:27638800-27640800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:27638800-27640800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:27639400-27640600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:27639400-27640600	Active TSS	Osteobl	bone
21	chr6:27639400-27640800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:27639400-27640800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr6:27639600-27640400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:27639600-27640600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:27639600-27640800	Active TSS	Hela-S3	cervix
26	chr6:27639600-27641000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:27639600-27641200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr6:27639600-27641400	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr6:27639600-27641400	Active TSS	A549	lung
30	chr6:27639600-27641600	Active TSS	K562	blood
31	chr6:27639800-27640400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr6:27639800-27640400	Active TSS	HepG2	liver
33	chr6:27639800-27640600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
34	chr6:27639800-27640600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
35	chr6:27639800-27640800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:27639800-27640800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
37	chr6:27639800-27640800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:27639800-27640800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:27639800-27640800	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr6:27639800-27641000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:27639800-27641000	Active TSS	HMEC	breast
42	chr6:27639800-27641000	Active TSS	NHEK	skin
43	chr6:27639800-27641200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr6:27640000-27640400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:27640000-27640400	Bivalent Enhancer	Primary B cells from cord blood	blood
46	chr6:27640000-27640400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr6:27640000-27640400	Bivalent/Poised TSS	Psoas Muscle	Psoas
48	chr6:27640000-27640400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
49	chr6:27640000-27640600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
50	chr6:27640000-27640600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood

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