Variant report

Variant	rs10955854
Chromosome Location	chr8:119098527-119098528
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SAMD12-4	chr8:119097734-119100498	NONHSAT128404

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11562756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17451540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17451547	0.82[ASN][1000 genomes]
rs2451133	0.85[JPT][hapmap]
rs2468136	0.85[JPT][hapmap]
rs2468137	0.85[JPT][hapmap]
rs55906753	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7835763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7836146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897829	0.85[JPT][hapmap]
rs921957	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1015380	chr8:118948652-119418389	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv539736	chr8:118948652-119418389	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv831441	chr8:119055370-119262970	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2752195	chr8:119058819-119139819	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv821660	chr8:119082062-119312183	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10955854	MAL2	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119075000-119102000	Weak transcription	Spleen	Spleen
2	chr8:119078000-119099000	Weak transcription	Dnd41	blood
3	chr8:119085600-119100200	Weak transcription	HSMMtube	muscle
4	chr8:119087600-119099200	Weak transcription	Pancreas	Pancrea
5	chr8:119087600-119101800	Weak transcription	Fetal Thymus	thymus
6	chr8:119087800-119098600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:119088000-119100200	Weak transcription	Aorta	Aorta
8	chr8:119088200-119102000	Weak transcription	Lung	lung
9	chr8:119088200-119102000	Weak transcription	Right Ventricle	heart
10	chr8:119088800-119099200	Weak transcription	Psoas Muscle	Psoas
11	chr8:119089200-119100400	Weak transcription	Fetal Stomach	stomach
12	chr8:119089600-119098600	Weak transcription	Ovary	ovary
13	chr8:119089600-119100400	Weak transcription	Fetal Muscle Leg	muscle
14	chr8:119089800-119102000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:119090000-119099200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr8:119090800-119102000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:119091800-119098600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr8:119092200-119099200	Weak transcription	Fetal Intestine Large	intestine
19	chr8:119092400-119100400	Weak transcription	HMEC	breast
20	chr8:119092400-119102000	Weak transcription	Gastric	stomach
21	chr8:119092400-119104800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr8:119092600-119098600	Weak transcription	NHEK	skin
23	chr8:119092600-119099000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:119092600-119100800	Weak transcription	HSMM	muscle
25	chr8:119092600-119110200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:119092800-119100200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr8:119093200-119099200	Weak transcription	Stomach Mucosa	stomach
28	chr8:119093200-119100200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr8:119093400-119098600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr8:119093600-119099400	Weak transcription	A549	lung
31	chr8:119093800-119102000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr8:119094000-119098600	Weak transcription	Small Intestine	intestine
33	chr8:119094000-119100000	Weak transcription	Fetal Intestine Small	intestine
34	chr8:119094000-119101000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr8:119094200-119098800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr8:119094200-119098800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr8:119094200-119100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr8:119094200-119117000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr8:119094400-119100200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr8:119094400-119110200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr8:119094600-119098600	Weak transcription	Primary T cells from cord blood	blood
42	chr8:119094600-119098600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr8:119094600-119099000	Weak transcription	Fetal Heart	heart
44	chr8:119094600-119102000	Weak transcription	Brain Angular Gyrus	brain
45	chr8:119094800-119100400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr8:119095400-119099600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr8:119095400-119100400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr8:119095800-119099600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr8:119095800-119102000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr8:119096000-119100200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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