Variant report

Variant	rs3087617
Chromosome Location	chr6:31556656-31556657
allele	A/T
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:5)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31552844..31558545-chr6:31585940..31590373,6	MCF-7	breast:
2	chr6:31523207..31526178-chr6:31556028..31558601,2	K562	blood:
3	chr6:31510286..31512313-chr6:31556327..31558851,2	K562	blood:
4	chr6:31497143..31499271-chr6:31555695..31557452,2	K562	blood:
5	chr6:31554501..31557206-chr6:31559378..31562333,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LST1-1	chr6:31554977-31556686	NONHSAT108793
2	lnc-LST1-1	chr6:31556295-31556686	NR_029461
3	lnc-LST1-1	chr6:31556340-31556686	NR_029462

No data

Variant related genes	Relation type
ENSG00000198563	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204475	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11753901	0.80[ASN][1000 genomes]
rs2509217	0.80[ASN][1000 genomes]
rs2515920	0.80[ASN][1000 genomes]
rs34744948	0.89[ASN][1000 genomes]
rs35266973	0.85[ASN][1000 genomes]
rs71563353	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
15	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS 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	326 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3087617	MICB	cis	Nerve Tibial	GTEx
rs3087617	MICB	cis	Heart Left Ventricle	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31550000-31583200	Weak transcription	Right Atrium	heart
2	chr6:31550200-31556800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:31550800-31560400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:31552600-31557200	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr6:31553400-31557000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr6:31553400-31557400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:31553400-31557600	Enhancers	K562	blood
8	chr6:31553600-31557000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:31554800-31557600	Enhancers	Fetal Muscle Trunk	muscle
10	chr6:31554800-31560400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:31555000-31557800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:31555200-31557200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:31555400-31557800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:31555600-31557000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:31555800-31557600	Enhancers	Fetal Muscle Leg	muscle
16	chr6:31555800-31558200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr6:31556000-31556800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr6:31556000-31557000	Enhancers	Colonic Mucosa	Colon
19	chr6:31556000-31557200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:31556000-31557200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:31556000-31557400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr6:31556000-31557800	Enhancers	Primary T cells from cord blood	blood
23	chr6:31556000-31557800	Genic enhancers	Spleen	Spleen
24	chr6:31556000-31560800	Weak transcription	Dnd41	blood
25	chr6:31556200-31557000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:31556200-31557000	Bivalent Enhancer	Adipose Nuclei	Adipose
27	chr6:31556200-31557000	Enhancers	Gastric	stomach
28	chr6:31556200-31557000	Enhancers	Left Ventricle	heart
29	chr6:31556200-31557200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
30	chr6:31556200-31557600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:31556200-31560200	Weak transcription	Thymus	Thymus
32	chr6:31556200-31560600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:31556200-31560600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr6:31556400-31556800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:31556400-31557000	Enhancers	HSMM	muscle
36	chr6:31556400-31557200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr6:31556400-31557400	Enhancers	Placenta	Placenta
38	chr6:31556400-31557400	Enhancers	NHDF-Ad	bronchial
39	chr6:31556400-31557600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:31556400-31557800	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:31556600-31557000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
42	chr6:31556600-31557200	Enhancers	Fetal Thymus	thymus
43	chr6:31556600-31557400	Enhancers	Primary hematopoietic stem cells	blood
44	chr6:31556600-31557400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr6:31556600-31557600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr6:31556600-31557600	Enhancers	GM12878-XiMat	blood
47	chr6:31556600-31557800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr6:31556600-31558000	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr6:31556600-31558000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:31556600-31558000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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