Variant report

Variant	rs6981540
Chromosome Location	chr8:1907855-1907856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:1907491..1909196-chr8:1911477..1913920,2	K562	blood:
2	chr8:1902551..1904412-chr8:1906073..1908055,2	K562	blood:
3	chr8:1906659..1908488-chr8:1948019..1949630,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CSMD1-18	chr8:1906704-1908609	l_3533_chr8:1906703-1909044_brain

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1043221	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1043225	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1043226	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11136448	1.00[ASN][1000 genomes]
rs11136454	1.00[ASN][1000 genomes]
rs11136467	1.00[CHB][hapmap]
rs13257924	1.00[CHB][hapmap]
rs13260541	1.00[ASN][1000 genomes]
rs13267164	1.00[ASN][1000 genomes]
rs13271878	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13272508	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13276575	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13279574	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14375	1.00[CHB][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs2004869	1.00[ASN][1000 genomes]
rs28414137	1.00[ASN][1000 genomes]
rs34295832	1.00[ASN][1000 genomes]
rs36144043	1.00[ASN][1000 genomes]
rs3824186	1.00[CHB][hapmap]
rs4448323	0.81[MEX][hapmap]
rs4546706	1.00[ASN][1000 genomes]
rs4598291	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs5025039	1.00[ASN][1000 genomes]
rs6558566	1.00[CHB][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs6984792	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6984824	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7015556	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73184743	1.00[ASN][1000 genomes]
rs73184745	1.00[ASN][1000 genomes]
rs73184750	1.00[ASN][1000 genomes]
rs73184755	1.00[ASN][1000 genomes]
rs73184756	1.00[ASN][1000 genomes]
rs73184758	1.00[ASN][1000 genomes]
rs7386016	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7386034	1.00[ASN][1000 genomes]
rs7386548	1.00[ASN][1000 genomes]
rs7386994	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7387198	1.00[ASN][1000 genomes]
rs9314443	1.00[ASN][1000 genomes]
rs9644316	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9650490	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889704	chr8:1563904-1965389	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv889707	chr8:1581839-1920461	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv889708	chr8:1581839-1965389	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv889709	chr8:1581839-1965389	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv889712	chr8:1591412-2337777	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv889714	chr8:1616718-1965389	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv609531	chr8:1717036-1965389	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv889717	chr8:1746950-1924237	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv889724	chr8:1756800-1965389	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv889729	chr8:1800560-1947417	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
11	nsv889731	chr8:1868842-1965389	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv889735	chr8:1892069-1907855	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv889736	chr8:1892069-1965389	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv889738	chr8:1897249-1965389	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv889739	chr8:1898547-1918352	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv609555	chr8:1904157-1913134	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv517213	chr8:1906630-1913134	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv524631	chr8:1907855-1916144	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6981540	LUC7L2	trans	parietal	SCAN
rs6981540	KBTBD11	cis	cerebellum	SCAN
rs6981540	OBP2B	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1845400-1908000	Weak transcription	Right Atrium	heart
2	chr8:1889400-1910000	Weak transcription	HUVEC	blood vessel
3	chr8:1890000-1911000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:1898400-1908600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:1900200-1909000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:1903600-1908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:1903600-1908400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr8:1903600-1909400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr8:1904000-1908000	Weak transcription	NHEK	skin
10	chr8:1904400-1908000	Strong transcription	Dnd41	blood
11	chr8:1905000-1909600	Enhancers	Liver	Liver
12	chr8:1905200-1908800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:1905400-1909000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr8:1905600-1908000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:1905600-1908400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:1905600-1910800	Weak transcription	Gastric	stomach
17	chr8:1905600-1921000	Weak transcription	Aorta	Aorta
18	chr8:1905800-1908200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr8:1905800-1916800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr8:1906000-1911200	Weak transcription	HMEC	breast
21	chr8:1906000-1914200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr8:1906400-1908000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr8:1906400-1908400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr8:1906400-1909200	Weak transcription	Thymus	Thymus
25	chr8:1906400-1910600	Weak transcription	Lung	lung
26	chr8:1906400-1911200	Weak transcription	Psoas Muscle	Psoas
27	chr8:1906400-1911400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr8:1906600-1908000	Weak transcription	NH-A	brain
29	chr8:1906600-1908200	Weak transcription	A549	lung
30	chr8:1906600-1908400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr8:1906600-1908400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr8:1906600-1908600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr8:1906600-1908800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr8:1906600-1910400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr8:1906600-1910800	Weak transcription	Brain Angular Gyrus	brain
36	chr8:1906600-1911000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr8:1906600-1911200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr8:1906600-1911200	Weak transcription	Brain Germinal Matrix	brain
39	chr8:1906600-1911400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr8:1906600-1914200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr8:1906600-1914200	Weak transcription	Colonic Mucosa	Colon
42	chr8:1906600-1914600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr8:1906600-1921000	Weak transcription	Right Ventricle	heart
44	chr8:1906800-1908200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr8:1906800-1908400	Weak transcription	Fetal Heart	heart
46	chr8:1906800-1908400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr8:1906800-1908800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr8:1906800-1910200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr8:1906800-1910600	Weak transcription	Brain Anterior Caudate	brain
50	chr8:1906800-1910600	Weak transcription	Brain Hippocampus Middle	brain

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