Variant report

Variant	rs557037
Chromosome Location	chr11:74562067-74562068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74552536..74554674-chr11:74560171..74562245,2	K562	blood:

Extended variants
information (count: 10 )
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];0.95[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];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs662035	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]
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[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs557037	SPCS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
2	chr11:74543800-74565800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum
4	chr11:74545600-74564600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr11:74545600-74568400	Strong transcription	Fetal Intestine Large	intestine
6	chr11:74545800-74565000	Strong transcription	Fetal Muscle Leg	muscle
7	chr11:74546000-74566800	Strong transcription	Fetal Stomach	stomach
8	chr11:74547600-74571400	Weak transcription	Fetal Brain Male	brain
9	chr11:74547800-74562800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:74549400-74567600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:74550600-74564600	Strong transcription	Fetal Intestine Small	intestine
12	chr11:74551000-74568400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr11:74552600-74565400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr11:74552800-74576800	Strong transcription	Stomach Smooth Muscle	stomach
15	chr11:74553800-74569400	Weak transcription	Fetal Heart	heart
16	chr11:74554200-74567600	Weak transcription	Psoas Muscle	Psoas
17	chr11:74554800-74571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:74555800-74569800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:74556800-74562400	Weak transcription	Hela-S3	cervix
20	chr11:74557200-74562800	Weak transcription	K562	blood
21	chr11:74558200-74563400	Strong transcription	Rectal Smooth Muscle	rectum
22	chr11:74558200-74564400	Strong transcription	Thymus	Thymus
23	chr11:74558200-74564600	Strong transcription	Dnd41	blood
24	chr11:74558200-74565200	Strong transcription	Colonic Mucosa	Colon
25	chr11:74558400-74564000	Strong transcription	Fetal Brain Female	brain
26	chr11:74558400-74564200	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:74558400-74564600	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr11:74558600-74563400	Strong transcription	Brain Anterior Caudate	brain
29	chr11:74558600-74563400	Strong transcription	Left Ventricle	heart
30	chr11:74558600-74563600	Strong transcription	Placenta	Placenta
31	chr11:74558600-74565000	Strong transcription	Primary T cells from cord blood	blood
32	chr11:74558600-74565800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:74558800-74564600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:74558800-74565400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:74558800-74567400	Weak transcription	Small Intestine	intestine
36	chr11:74559000-74571400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:74559200-74562200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:74559200-74562400	Weak transcription	Ovary	ovary
39	chr11:74559200-74562400	Weak transcription	Spleen	Spleen
40	chr11:74559200-74565400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:74559200-74571400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:74559200-74571800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:74559400-74562600	Weak transcription	Aorta	Aorta
44	chr11:74559400-74562600	Weak transcription	Lung	lung
45	chr11:74559400-74570000	Weak transcription	Right Ventricle	heart
46	chr11:74559600-74562400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:74559600-74562800	Weak transcription	Gastric	stomach
48	chr11:74559800-74562200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:74559800-74562600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr11:74560200-74562400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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