Variant report

Variant	rs10110144
Chromosome Location	chr8:121005715-121005716
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1051534	0.80[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap]
rs10955946	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10955947	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11779963	0.88[ASN][1000 genomes]
rs11787175	0.81[CHD][hapmap];0.82[MEX][hapmap]
rs11787250	0.81[CHD][hapmap];0.82[MEX][hapmap]
rs11984766	0.82[MEX][hapmap]
rs11986202	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11995866	0.80[CEU][hapmap]
rs12680396	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13266382	0.83[AMR][1000 genomes]
rs13272368	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1356748	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2139434	0.84[AMR][1000 genomes]
rs2139435	0.89[ASN][1000 genomes]
rs2139436	0.89[ASN][1000 genomes]
rs2139437	0.81[ASN][1000 genomes]
rs2326429	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650977	0.86[AMR][1000 genomes]
rs4053282	0.80[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4398969	0.89[ASN][1000 genomes]
rs4584180	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870969	0.87[ASN][1000 genomes]
rs4870970	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4871719	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4871819	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4871821	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871823	0.85[ASN][1000 genomes]
rs4871824	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4871827	0.84[CHD][hapmap];0.82[MEX][hapmap]
rs58564644	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60657932	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62528700	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469889	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6469890	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.84[ASN][1000 genomes]
rs6997067	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7833689	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7836124	0.82[EUR][1000 genomes]
rs7836786	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs9642847	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9643139	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9643140	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv891419	chr8:120990455-121047798	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3348294	chr8:121000288-121250984	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10110144	ATAD2	cis	parietal	SCAN
rs10110144	DSCC1	cis	parietal	SCAN
rs10110144	DSCC1	cis	cerebellum	SCAN
rs10110144	DEPDC6	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120978000-121013600	Weak transcription	Gastric	stomach
2	chr8:120991200-121013400	Weak transcription	Fetal Stomach	stomach
3	chr8:120995600-121038400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr8:120995800-121013800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr8:121000600-121019600	Weak transcription	Left Ventricle	heart
6	chr8:121001800-121015600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr8:121001800-121021200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr8:121002600-121006000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr8:121002800-121006000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr8:121003200-121006600	Enhancers	Rectal Smooth Muscle	rectum
11	chr8:121003200-121015200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr8:121003200-121015200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr8:121003600-121013400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr8:121003600-121013400	Weak transcription	Fetal Intestine Small	intestine
15	chr8:121003600-121013600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr8:121003600-121015200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr8:121003800-121007000	Enhancers	Colon Smooth Muscle	Colon
18	chr8:121003800-121013400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr8:121003800-121014800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr8:121003800-121015200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr8:121004000-121013800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr8:121004000-121017600	Weak transcription	Right Atrium	heart
23	chr8:121004000-121048000	Weak transcription	Stomach Mucosa	stomach
24	chr8:121004600-121013400	Weak transcription	Fetal Muscle Leg	muscle
25	chr8:121004600-121013600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr8:121004600-121015200	Weak transcription	Brain Anterior Caudate	brain
27	chr8:121004600-121041400	Weak transcription	Brain Angular Gyrus	brain
28	chr8:121004800-121017400	Weak transcription	Fetal Kidney	kidney
29	chr8:121005000-121013600	Weak transcription	Ovary	ovary
30	chr8:121005200-121011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr8:121005200-121012400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:121005200-121015200	Weak transcription	Spleen	Spleen
33	chr8:121005200-121045800	Weak transcription	Psoas Muscle	Psoas
34	chr8:121005400-121005800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr8:121005400-121005800	Enhancers	Brain Substantia Nigra	brain
36	chr8:121005400-121006400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr8:121005400-121006400	Enhancers	Brain Hippocampus Middle	brain
38	chr8:121005600-121005800	Enhancers	Osteobl	bone
39	chr8:121005600-121006000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr8:121005600-121012200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr8:121005600-121015600	Weak transcription	Adipose Nuclei	Adipose

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