Variant report

Variant	rs3910384
Chromosome Location	chr11:9599943-9599944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:9593829-9601404	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr11:9598235-9600331	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr11:9599843-9600362	MCF10A-Er-Src	breast:	n/a	n/a
4	CHD1	chr11:9594023-9600398	IMR90	lung:	n/a	chr11:9596149-9596159
5	POLR2A	chr11:9599923-9600381	A549	lung:	n/a	n/a
6	POLR2A	chr11:9592789-9600461	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr11:9599736-9604122	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr11:9597964-9600379	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9593380..9601954-chr11:9626466..9639393,32	K562	blood:
2	chr11:9482164..9483690-chr11:9598599..9601195,2	MCF-7	breast:
3	chr11:9481508..9485106-chr11:9595203..9601095,6	MCF-7	breast:

Variant related genes	Relation type
WEE1	TF binding region
RN7SL56P	TF binding region
ENSG00000166478	Chromatin interaction
ENSG00000243964	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3763868	0.87[ASN][1000 genomes]
rs3763869	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.83[ASN][1000 genomes]
rs3870635	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4370932	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6486433	0.86[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	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3910384	MICAL2	cis	parietal	SCAN
rs3910384	SWAP70	cis	lymphoblastoid	seeQTL
rs3910384	PTH	cis	cerebellum	SCAN
rs3910384	SWAP70	cis	multi-tissue	Pritchard
rs3910384	SWAP70	Cis_1M	lymphoblastoid	RTeQTL
rs3910384	SNORA23	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9594200-9600000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:9594200-9601200	Active TSS	Aorta	Aorta
3	chr11:9594800-9600000	Active TSS	Fetal Intestine Large	intestine
4	chr11:9596200-9600200	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr11:9596200-9600400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
6	chr11:9596400-9600200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
7	chr11:9596400-9600400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:9596600-9600400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
9	chr11:9596600-9601400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
10	chr11:9596800-9604000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:9597000-9600000	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr11:9597000-9600200	Active TSS	Stomach Smooth Muscle	stomach
13	chr11:9597000-9604600	Weak transcription	Lung	lung
14	chr11:9597000-9606000	Weak transcription	Small Intestine	intestine
15	chr11:9597000-9613400	Weak transcription	Gastric	stomach
16	chr11:9597000-9622000	Weak transcription	Spleen	Spleen
17	chr11:9597200-9600200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:9597200-9635000	Weak transcription	Pancreas	Pancrea
19	chr11:9597600-9601800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:9597600-9602000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:9597600-9602400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:9597600-9604200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:9597600-9609600	Weak transcription	Brain Anterior Caudate	brain
24	chr11:9597600-9615200	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:9597800-9600000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:9597800-9603400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr11:9597800-9604600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:9597800-9605600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr11:9598000-9600000	Transcr. at gene 5' and 3'	NHEK	skin
30	chr11:9598000-9600200	Transcr. at gene 5' and 3'	NH-A	brain
31	chr11:9598000-9605600	Weak transcription	Stomach Mucosa	stomach
32	chr11:9598200-9600000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:9598200-9600000	Transcr. at gene 5' and 3'	HSMM	muscle
34	chr11:9598400-9600200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr11:9598400-9612000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:9598600-9600000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:9598600-9600000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:9598600-9608800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:9598600-9610800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr11:9598800-9611600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr11:9599000-9600000	Strong transcription	Liver	Liver
42	chr11:9599000-9600200	Transcr. at gene 5' and 3'	HMEC	breast
43	chr11:9599000-9600400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
44	chr11:9599000-9600400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
45	chr11:9599000-9601200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
46	chr11:9599200-9600000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr11:9599200-9600400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:9599200-9600400	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
49	chr11:9599200-9601200	Genic enhancers	HepG2	liver
50	chr11:9599200-9606200	Weak transcription	Fetal Brain Male	brain

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