Variant report

Variant	rs3935784
Chromosome Location	chr16:74604841-74604842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:74582009..74584400-chr16:74603645..74605956,2	K562	blood:
2	chr16:74596930..74600415-chr16:74601800..74606565,4	K562	blood:
3	chr16:74604462..74608265-chr16:74639242..74641794,3	MCF-7	breast:
4	chr16:74596898..74600109-chr16:74602144..74605805,4	K562	blood:

Variant related genes	Relation type
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11149759	0.89[CEU][hapmap];0.85[GIH][hapmap];0.96[MEX][hapmap]
rs11643608	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2078330	0.81[JPT][hapmap]
rs2303279	0.94[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948443	chr16:73994997-74627711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
3	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv1060629	chr16:74483574-74660669	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv833279	chr16:74490746-74663073	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	nsv906905	chr16:74527618-74679244	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3935784	GLG1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74563200-74622400	Weak transcription	Fetal Stomach	stomach
2	chr16:74583000-74617200	Weak transcription	Fetal Muscle Leg	muscle
3	chr16:74587600-74612200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:74588200-74623200	Weak transcription	Primary B cells from cord blood	blood
5	chr16:74589800-74626800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr16:74590000-74607000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:74590200-74614600	Weak transcription	Adipose Nuclei	Adipose
8	chr16:74590400-74607600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr16:74591000-74624000	Weak transcription	Aorta	Aorta
10	chr16:74591800-74613600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr16:74593200-74608600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr16:74593800-74607200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr16:74595000-74622600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr16:74595200-74607000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr16:74595200-74607400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr16:74595800-74605000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr16:74595800-74608400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr16:74596000-74614400	Weak transcription	Colon Smooth Muscle	Colon
19	chr16:74596200-74607200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr16:74596200-74609400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr16:74596400-74607800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:74598000-74608600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr16:74598200-74606000	Weak transcription	Lung	lung
24	chr16:74598200-74607600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr16:74598200-74609200	Weak transcription	A549	lung
26	chr16:74598400-74607600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr16:74598600-74622600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:74598800-74606000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr16:74599000-74611000	Weak transcription	Spleen	Spleen
30	chr16:74599600-74623400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr16:74599800-74607800	Weak transcription	GM12878-XiMat	blood
32	chr16:74600000-74607600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr16:74600200-74616800	Weak transcription	Fetal Kidney	kidney
34	chr16:74601000-74607000	Enhancers	Primary T cells fromperipheralblood	blood
35	chr16:74601200-74606600	Weak transcription	Fetal Brain Male	brain
36	chr16:74601800-74606800	Enhancers	Pancreas	Pancrea
37	chr16:74602200-74607400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr16:74602600-74605400	Enhancers	Fetal Intestine Small	intestine
39	chr16:74603000-74606400	Enhancers	Gastric	stomach
40	chr16:74603400-74605000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr16:74603400-74610800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr16:74603400-74611800	Weak transcription	NHDF-Ad	bronchial
43	chr16:74603400-74611800	Weak transcription	Osteobl	bone
44	chr16:74603600-74606200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr16:74603600-74608000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr16:74603600-74610000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr16:74603800-74607800	Weak transcription	NHEK	skin
48	chr16:74604000-74605400	Enhancers	Brain Cingulate Gyrus	brain
49	chr16:74604000-74605400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr16:74604000-74606000	Enhancers	Primary T cells from cord blood	blood

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