Variant report

Variant	rs28732144
Chromosome Location	chr6:31556205-31556206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr6:31497143..31499271-chr6:31555695..31557452,2	K562	blood:
4	chr6:31554501..31557206-chr6:31559378..31562333,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LST1-1	chr6:31554977-31556686	NONHSAT108793

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

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs17207190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516474	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28381344	0.83[AMR][1000 genomes]
rs28732141	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732142	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28732145	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28732153	0.83[AMR][1000 genomes]
rs28732155	0.83[AMR][1000 genomes]
rs28732156	0.83[AMR][1000 genomes]
rs28732159	0.83[AMR][1000 genomes]
rs28732160	0.83[AMR][1000 genomes]
rs28895015	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905741	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3021366	1.00[ASN][1000 genomes]
rs3093661	0.95[EUR][1000 genomes]
rs3093668	0.97[EUR][1000 genomes]
rs3093726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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]
rs41293887	0.85[EUR][1000 genomes]
rs41293891	0.81[EUR][1000 genomes]
rs41293895	0.90[EUR][1000 genomes]
rs41293899	0.90[EUR][1000 genomes]
rs41293907	0.90[EUR][1000 genomes]
rs41293911	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293915	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41293919	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41293923	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41315808	0.83[AMR][1000 genomes]
rs4947326	0.83[EUR][1000 genomes]
rs4947327	0.83[EUR][1000 genomes]
rs4959077	0.85[EUR][1000 genomes]
rs4959078	0.90[EUR][1000 genomes]
rs7757162	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757383	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9267497	0.83[EUR][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs28732144	MICB	cis	Heart Left Ventricle	GTEx
rs28732144	MICA///MICB	N/A	lymphoblastoid	RTeQTL
rs28732144	MICB	cis	Adipose Subcutaneous	GTEx
rs28732144	MICB	Cis_1M	lymphoblastoid	RTeQTL
rs28732144	MICB	cis	Nerve Tibial	GTEx
rs28732144	MICB	cis	Thyroid	GTEx
rs28732144	MICB	cis	Whole Blood	GTEx
rs28732144	XXbac-BPG181B23.7	cis	Whole Blood	GTEx

Chromatin state (count:53 , 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	chr6:31553000-31556400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr6:31553200-31556600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr6:31553400-31556600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:31553400-31557000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr6:31553400-31557400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:31553400-31557600	Enhancers	K562	blood
11	chr6:31553600-31556600	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr6:31553600-31556600	Flanking Active TSS	Fetal Thymus	thymus
13	chr6:31553600-31557000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:31553800-31556400	Weak transcription	Liver	Liver
15	chr6:31554000-31556600	Flanking Active TSS	GM12878-XiMat	blood
16	chr6:31554200-31556400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:31554200-31556400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:31554600-31556400	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr6:31554800-31557600	Enhancers	Fetal Muscle Trunk	muscle
20	chr6:31554800-31560400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:31555000-31557800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:31555200-31556400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:31555200-31557200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:31555400-31557800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:31555600-31556400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:31555600-31556600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr6:31555600-31557000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:31555800-31556600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:31555800-31557600	Enhancers	Fetal Muscle Leg	muscle
30	chr6:31555800-31558200	Enhancers	Primary T cells fromperipheralblood	blood
31	chr6:31556000-31556600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
32	chr6:31556000-31556800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr6:31556000-31557000	Enhancers	Colonic Mucosa	Colon
34	chr6:31556000-31557200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr6:31556000-31557200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:31556000-31557400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr6:31556000-31557800	Enhancers	Primary T cells from cord blood	blood
38	chr6:31556000-31557800	Genic enhancers	Spleen	Spleen
39	chr6:31556000-31560800	Weak transcription	Dnd41	blood
40	chr6:31556200-31556400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:31556200-31556400	Bivalent Enhancer	Placenta	Placenta
42	chr6:31556200-31556400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
43	chr6:31556200-31556600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:31556200-31556600	Enhancers	Duodenum Mucosa	Duodenum
45	chr6:31556200-31557000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:31556200-31557000	Bivalent Enhancer	Adipose Nuclei	Adipose
47	chr6:31556200-31557000	Enhancers	Gastric	stomach
48	chr6:31556200-31557000	Enhancers	Left Ventricle	heart
49	chr6:31556200-31557200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
50	chr6:31556200-31557600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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