Variant report

Variant	rs3093661
Chromosome Location	chr6:31543758-31543759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31543436..31546085-chr6:31623244..31625414,2	MCF-7	breast:
2	chr6:31507998..31511841-chr6:31541735..31545245,5	MCF-7	breast:
3	chr6:31542672..31544804-chr6:31702664..31704373,2	MCF-7	breast:
4	chr6:31542598..31545129-chr6:31587096..31589564,4	MCF-7	breast:
5	chr17:56708437..56711431-chr6:31543169..31545000,2	MCF-7	breast:
6	chr12:120729043..120729757-chr6:31543246..31544060,2	NB4	blood:

Variant related genes	Relation type
ENSG00000204469	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000204444	Chromatin interaction
ENSG00000265236	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs17207190	0.95[EUR][1000 genomes]
rs2516474	0.93[EUR][1000 genomes]
rs2734576	0.94[ASN][1000 genomes]
rs28732141	0.98[EUR][1000 genomes]
rs28732142	0.98[EUR][1000 genomes]
rs28732143	0.98[EUR][1000 genomes]
rs28732144	0.95[EUR][1000 genomes]
rs28732145	0.90[EUR][1000 genomes]
rs28895015	0.90[EUR][1000 genomes]
rs3093662	1.00[ASN][1000 genomes]
rs3093664	1.00[ASN][1000 genomes]
rs3093668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3093726	0.98[EUR][1000 genomes]
rs3093727	0.98[EUR][1000 genomes]
rs361525	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3828917	0.81[EUR][1000 genomes]
rs41293856	0.81[EUR][1000 genomes]
rs41293860	0.81[EUR][1000 genomes]
rs41293879	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41293887	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41293891	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41293895	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41293899	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41293907	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41293911	0.93[EUR][1000 genomes]
rs41293915	0.93[EUR][1000 genomes]
rs41293919	0.93[EUR][1000 genomes]
rs41293923	0.93[EUR][1000 genomes]
rs4947326	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4947327	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4959077	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4959078	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4959079	0.94[ASN][1000 genomes]
rs7757162	0.86[EUR][1000 genomes]
rs7757383	0.86[EUR][1000 genomes]
rs9267454	0.94[ASN][1000 genomes]
rs9267456	0.94[ASN][1000 genomes]
rs9267462	0.94[ASN][1000 genomes]
rs9267463	0.94[ASN][1000 genomes]
rs9267464	0.94[ASN][1000 genomes]
rs9267465	0.94[ASN][1000 genomes]
rs9267466	0.94[ASN][1000 genomes]
rs9267487	0.94[ASN][1000 genomes]
rs9267492	0.94[ASN][1000 genomes]
rs9267497	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9267499	0.85[ASN][1000 genomes]
rs9267502	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers 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 miRNA target site	334 gene(s)	inside rSNPs	diseases
3	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
4	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
5	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
6	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
7	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
8	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
9	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
10	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
11	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
12	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
13	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
14	nsv470809	chr6:31496915-31544189	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
15	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
16	nsv462870	chr6:31528130-31544189	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv601941	chr6:31528130-31544189	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3093661	MICB	cis	Nerve Tibial	GTEx
rs3093661	MICB	cis	Heart Left Ventricle	GTEx
rs3093661	XXbac-BPG181B23.7	cis	Whole Blood	GTEx
rs3093661	MICB	cis	Whole Blood	GTEx
rs3093661	HCP5	cis	lymphoblastoid	seeQTL
rs3093661	MICB	cis	Thyroid	GTEx
rs3093661	MICB	cis	Adipose Subcutaneous	GTEx
rs3093661	MICB	cis	lymphoblastoid	seeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31536000-31546200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:31536000-31548400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:31536600-31544200	Weak transcription	K562	blood
4	chr6:31540200-31548000	Weak transcription	Small Intestine	intestine
5	chr6:31541400-31546200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:31542400-31545200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr6:31542800-31543800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr6:31542800-31543800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr6:31542800-31543800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr6:31542800-31544000	Active TSS	Stomach Smooth Muscle	stomach
11	chr6:31542800-31544600	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr6:31542800-31544600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr6:31542800-31545200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr6:31543000-31543800	Bivalent/Poised TSS	Colonic Mucosa	Colon
15	chr6:31543000-31544400	Enhancers	HSMMtube	muscle
16	chr6:31543000-31544600	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr6:31543000-31544600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:31543000-31544800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr6:31543000-31545400	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr6:31543200-31543800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:31543200-31543800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr6:31543200-31543800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:31543200-31543800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:31543200-31543800	Active TSS	Left Ventricle	heart
25	chr6:31543200-31543800	Active TSS	Psoas Muscle	Psoas
26	chr6:31543200-31543800	Flanking Active TSS	Thymus	Thymus
27	chr6:31543200-31543800	Flanking Active TSS	NHEK	skin
28	chr6:31543200-31543800	Bivalent/Poised TSS	Osteobl	bone
29	chr6:31543200-31544000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:31543200-31544000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:31543200-31544000	Active TSS	Right Ventricle	heart
32	chr6:31543200-31544200	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr6:31543200-31544600	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr6:31543200-31544800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr6:31543200-31544800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:31543200-31544800	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr6:31543200-31545000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:31543200-31545000	Flanking Active TSS	Fetal Thymus	thymus
39	chr6:31543200-31545200	Active TSS	Rectal Smooth Muscle	rectum
40	chr6:31543400-31543800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:31543400-31543800	Active TSS	Brain Anterior Caudate	brain
42	chr6:31543400-31543800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr6:31543400-31543800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
44	chr6:31543400-31543800	Flanking Bivalent TSS/Enh	Placenta	Placenta
45	chr6:31543400-31543800	Active TSS	Gastric	stomach
46	chr6:31543400-31543800	Active TSS	Lung	lung
47	chr6:31543400-31543800	Flanking Bivalent TSS/Enh	Dnd41	blood
48	chr6:31543400-31543800	Flanking Active TSS	HMEC	breast
49	chr6:31543400-31544000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr6:31543400-31544000	Active TSS	Brain Hippocampus Middle	brain

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