Variant report

Variant	rs4930561
Chromosome Location	chr11:67931761-67931762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:67928130..67930692-chr11:67930944..67932522,2	MCF-7	breast:
2	chr11:67887292..67890781-chr11:67931037..67935551,5	K562	blood:
3	chr11:67929250..67931761-chr11:67939432..67941262,2	K562	blood:
4	chr11:67797783..67800702-chr11:67930792..67932845,2	MCF-7	breast:
5	chr11:67887183..67889702-chr11:67931726..67933755,2	MCF-7	breast:
6	chr11:67794907..67797094-chr11:67930115..67932239,2	MCF-7	breast:
7	chr11:67922850..67924988-chr11:67930230..67933194,2	K562	blood:
8	chr11:67928423..67930737-chr11:67930879..67934673,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000110717	Chromatin interaction
ENSG00000110721	Chromatin interaction
ENSG00000255306	Chromatin interaction
ENSG00000255236	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10791957	0.81[MEX][hapmap]
rs10896298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896299	0.82[CEU][hapmap]
rs10896301	0.85[ASN][1000 genomes]
rs10896303	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10896304	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10896305	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11228131	0.81[MEX][hapmap]
rs11228145	0.80[JPT][hapmap]
rs12225316	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1894204	0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs2011157	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2054865	0.87[ASN][1000 genomes]
rs2457179	0.81[MEX][hapmap]
rs2511437	0.81[MEX][hapmap]
rs2511467	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs2511469	0.80[JPT][hapmap]
rs2511470	0.81[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs2511475	0.80[JPT][hapmap];0.85[MEX][hapmap]
rs2511478	0.80[ASN][1000 genomes]
rs2511479	0.80[JPT][hapmap]
rs2512611	0.81[MEX][hapmap]
rs2512612	0.81[MEX][hapmap]
rs2512623	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs3133327	0.81[MEX][hapmap]
rs34236202	0.86[ASN][1000 genomes]
rs34493482	0.87[ASN][1000 genomes]
rs4073551	0.81[MEX][hapmap]
rs4345973	0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4930228	0.83[AMR][1000 genomes]
rs4930229	0.93[ASN][1000 genomes]
rs4930230	0.89[ASN][1000 genomes]
rs4930563	0.88[ASN][1000 genomes]
rs4930564	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61890513	0.84[ASN][1000 genomes]
rs7931502	0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs7940501	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs7944372	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs7950452	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4930561	SYT12	cis	cerebellum	SCAN
rs4930561	FGF19	cis	parietal	SCAN
rs4930561	SUV420H1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67913200-67933200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr11:67915000-67933000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:67915000-67934000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:67915000-67943000	Weak transcription	Right Atrium	heart
5	chr11:67915000-67973800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:67917200-67939400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:67918000-67931800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:67918000-67931800	Weak transcription	Hela-S3	cervix
9	chr11:67918000-67933200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:67918800-67936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr11:67922000-67937200	Weak transcription	Stomach Mucosa	stomach
12	chr11:67922000-67937400	Weak transcription	Small Intestine	intestine
13	chr11:67922400-67933200	Weak transcription	Fetal Brain Male	brain
14	chr11:67922600-67956600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr11:67922800-67933200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:67924000-67933600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr11:67924000-67933800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:67924000-67936200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:67924200-67949800	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr11:67924400-67956600	Strong transcription	Fetal Intestine Large	intestine
21	chr11:67924400-67956800	Strong transcription	Primary T cells from cord blood	blood
22	chr11:67924400-67957000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:67924600-67956400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr11:67924600-67956600	Strong transcription	Fetal Muscle Leg	muscle
25	chr11:67924800-67943200	Strong transcription	Brain Substantia Nigra	brain
26	chr11:67925000-67932000	Strong transcription	Fetal Thymus	thymus
27	chr11:67925000-67933000	Strong transcription	Liver	Liver
28	chr11:67925200-67955000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr11:67925600-67933200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:67925600-67944400	Strong transcription	Fetal Intestine Small	intestine
31	chr11:67925600-67948400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:67925800-67933000	Weak transcription	HUVEC	blood vessel
33	chr11:67926200-67931800	Weak transcription	Brain Angular Gyrus	brain
34	chr11:67926200-67932000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr11:67926200-67933000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:67926200-67933200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr11:67926200-67933800	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:67926400-67931800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:67926400-67931800	Weak transcription	NHDF-Ad	bronchial
40	chr11:67926400-67933000	Weak transcription	Ovary	ovary
41	chr11:67926400-67933800	Weak transcription	Psoas Muscle	Psoas
42	chr11:67926600-67933200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:67926600-67933400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr11:67926800-67933000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:67926800-67933200	Weak transcription	GM12878-XiMat	blood
46	chr11:67927800-67934800	Strong transcription	Fetal Lung	lung
47	chr11:67928000-67934000	Weak transcription	Fetal Heart	heart
48	chr11:67928000-67935000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:67928000-67956600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr11:67928400-67932000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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