Variant report

Variant	rs662035
Chromosome Location	chr11:74604918-74604919
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs478280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs557037	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs572656	0.87[GIH][hapmap];1.00[JPT][hapmap]
rs578090	0.83[JPT][hapmap]
rs592823	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs658623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs693275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
2	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs662035	SPCS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74587400-74611800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:74587400-74629600	Weak transcription	Gastric	stomach
3	chr11:74588400-74605400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr11:74588400-74606200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr11:74588400-74630600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr11:74588400-74636000	Weak transcription	NHLF	lung
7	chr11:74591800-74606000	Weak transcription	Right Ventricle	heart
8	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
9	chr11:74595600-74606600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:74595800-74605200	Weak transcription	Brain Anterior Caudate	brain
11	chr11:74595800-74611800	Weak transcription	Brain Angular Gyrus	brain
12	chr11:74596200-74605000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:74596200-74606200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:74596400-74606200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:74596400-74612000	Weak transcription	HSMM	muscle
16	chr11:74596800-74619000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:74597600-74606200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:74598000-74606600	Weak transcription	Psoas Muscle	Psoas
19	chr11:74598000-74606800	Weak transcription	Left Ventricle	heart
20	chr11:74598200-74606200	Weak transcription	NHEK	skin
21	chr11:74598200-74609800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:74598200-74615200	Weak transcription	Osteobl	bone
23	chr11:74598400-74606200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:74598400-74606400	Weak transcription	Primary B cells from cord blood	blood
25	chr11:74598400-74611800	Weak transcription	Dnd41	blood
26	chr11:74598400-74629600	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:74598800-74607400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr11:74599000-74605000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:74599000-74606200	Weak transcription	Thymus	Thymus
30	chr11:74599000-74606800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:74599000-74607000	Weak transcription	Ovary	ovary
32	chr11:74599000-74611800	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:74599200-74605400	Weak transcription	Aorta	Aorta
34	chr11:74599200-74606200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:74599200-74606200	Weak transcription	Fetal Intestine Large	intestine
36	chr11:74599200-74606600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:74599200-74607400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:74599200-74611600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:74599200-74619400	Weak transcription	Colonic Mucosa	Colon
40	chr11:74599400-74605600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:74599400-74606200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:74599400-74606200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:74599400-74606200	Weak transcription	Pancreas	Pancrea
44	chr11:74599400-74606400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:74599400-74606600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:74599400-74606800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:74599400-74611800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:74599600-74605000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:74599600-74606200	Weak transcription	Fetal Stomach	stomach
50	chr11:74599600-74606200	Weak transcription	Lung	lung

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