Variant report

Variant	rs3093662
Chromosome Location	chr6:31544189-31544190
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	chr6:31508160..31511245-chr6:31544123..31545855,4	K562	blood:
3	chr6:31507998..31511841-chr6:31541735..31545245,5	MCF-7	breast:
4	chr6:31508652..31510953-chr6:31543924..31545727,2	K562	blood:
5	chr6:31542672..31544804-chr6:31702664..31704373,2	MCF-7	breast:
6	chr6:31542598..31545129-chr6:31587096..31589564,4	MCF-7	breast:
7	chr17:56708437..56711431-chr6:31543169..31545000,2	MCF-7	breast:

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

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs2734576	0.94[ASN][1000 genomes]
rs3093553	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs3093661	1.00[ASN][1000 genomes]
rs3093664	1.00[ASN][1000 genomes]
rs3093668	0.88[ASN][1000 genomes]
rs361525	1.00[ASN][1000 genomes]
rs41293879	0.88[ASN][1000 genomes]
rs41293887	0.88[ASN][1000 genomes]
rs41293891	0.88[ASN][1000 genomes]
rs41293895	0.88[ASN][1000 genomes]
rs41293899	0.94[ASN][1000 genomes]
rs41293907	0.94[ASN][1000 genomes]
rs4947326	0.94[ASN][1000 genomes]
rs4947327	0.94[ASN][1000 genomes]
rs4959077	0.88[ASN][1000 genomes]
rs4959078	0.94[ASN][1000 genomes]
rs4959079	0.94[ASN][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	0.94[ASN][1000 genomes]
rs9267499	0.85[ASN][1000 genomes]
rs9267502	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3093662	MICB	cis	Heart Left Ventricle	GTEx
rs3093662	MICB	cis	lymphoblastoid	seeQTL
rs3093662	XXbac-BPG181B23.7	cis	Whole Blood	GTEx

Chromatin state (count:68 , 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	chr6:31542800-31544600	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr6:31542800-31544600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr6:31542800-31545200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr6:31543000-31544400	Enhancers	HSMMtube	muscle
11	chr6:31543000-31544600	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr6:31543000-31544600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:31543000-31544800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr6:31543000-31545400	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr6:31543200-31544200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr6:31543200-31544600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr6:31543200-31544800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr6:31543200-31544800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:31543200-31544800	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr6:31543200-31545000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:31543200-31545000	Flanking Active TSS	Fetal Thymus	thymus
22	chr6:31543200-31545200	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:31543400-31544200	Active TSS	Colon Smooth Muscle	Colon
24	chr6:31543400-31544400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:31543400-31544400	Active TSS	Liver	Liver
26	chr6:31543400-31544400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
27	chr6:31543400-31544400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
28	chr6:31543400-31544600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:31543400-31544800	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:31543400-31545000	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr6:31543400-31545000	Active TSS	Esophagus	oesophagus
32	chr6:31543400-31546000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:31543400-31546800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:31543600-31544200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr6:31543600-31544200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:31543600-31544200	Active TSS	Right Atrium	heart
37	chr6:31543600-31544400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr6:31543600-31544600	Active TSS	GM12878-XiMat	blood
39	chr6:31543600-31544800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
40	chr6:31543600-31545000	Active TSS	Adipose Nuclei	Adipose
41	chr6:31543600-31546800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
42	chr6:31543800-31544200	Active TSS	Primary T cells fromperipheralblood	blood
43	chr6:31543800-31544400	Flanking Active TSS	Dnd41	blood
44	chr6:31543800-31544600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:31543800-31544600	Bivalent/Poised TSS	Placenta	Placenta
46	chr6:31543800-31544800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:31543800-31544800	Weak transcription	Gastric	stomach
48	chr6:31543800-31544800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr6:31543800-31545200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:31543800-31545400	Enhancers	Primary hematopoietic stem cells	blood

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