Variant report

Variant	rs658623
Chromosome Location	chr11:74567491-74567492
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74565498..74567871-chr11:74571743..74574141,2	K562	blood:

Extended variants
information (count: 11 )
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];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557037	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]
rs572656	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs578090	0.83[JPT][hapmap]
rs592823	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs662035	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];1.00[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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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
rs658623	SPCS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 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	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum
3	chr11:74545600-74568400	Strong transcription	Fetal Intestine Large	intestine
4	chr11:74547600-74571400	Weak transcription	Fetal Brain Male	brain
5	chr11:74549400-74567600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:74551000-74568400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr11:74552800-74576800	Strong transcription	Stomach Smooth Muscle	stomach
8	chr11:74553800-74569400	Weak transcription	Fetal Heart	heart
9	chr11:74554200-74567600	Weak transcription	Psoas Muscle	Psoas
10	chr11:74554800-74571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:74555800-74569800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:74559000-74571400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr11:74559200-74571400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:74559200-74571800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:74559400-74570000	Weak transcription	Right Ventricle	heart
16	chr11:74560200-74569800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:74560600-74571200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr11:74561000-74567800	Weak transcription	Brain Angular Gyrus	brain
19	chr11:74561200-74571200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr11:74561400-74568600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:74561600-74571200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:74561800-74571000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:74562000-74568200	Strong transcription	NHEK	skin
24	chr11:74562000-74571600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:74562200-74568400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:74562200-74570000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:74562200-74595800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:74562400-74570400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:74562600-74569600	Weak transcription	Fetal Kidney	kidney
30	chr11:74563000-74569600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr11:74563000-74571400	Weak transcription	Fetal Thymus	thymus
32	chr11:74563200-74567600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:74563200-74567600	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:74563200-74570200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr11:74563200-74571800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:74563200-74573600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:74563400-74567600	Weak transcription	Brain Anterior Caudate	brain
38	chr11:74563400-74567600	Weak transcription	Gastric	stomach
39	chr11:74563400-74567800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:74563400-74569600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:74563400-74569600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:74563400-74569800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:74563400-74570000	Weak transcription	K562	blood
44	chr11:74563400-74576600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:74563600-74567600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr11:74563600-74576400	Weak transcription	Colon Smooth Muscle	Colon
47	chr11:74563800-74567800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:74563800-74570000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr11:74564000-74567800	Weak transcription	Fetal Brain Female	brain
50	chr11:74564000-74569600	Weak transcription	Brain Germinal Matrix	brain

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