Variant report

Variant	rs10838703
Chromosome Location	chr11:47422861-47422862
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47207092..47208885-chr11:47420633..47423542,2	K562	blood:
2	chr11:47420444..47424832-chr11:47425633..47430159,5	MCF-7	breast:
3	chr11:47397121..47400538-chr11:47420513..47424481,4	K562	blood:

Variant related genes	Relation type
ENSG00000165915	Chromatin interaction
ENSG00000066336	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11039149	0.81[MEX][hapmap]
rs11039244	0.92[CEU][hapmap]
rs11039266	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap]
rs11606287	0.84[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12224672	0.86[AMR][1000 genomes]
rs12361415	1.00[ASW][hapmap];0.83[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12577643	0.94[CEU][hapmap]
rs2278890	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs2280231	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap]
rs2293576	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35032070	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7103835	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv541034	chr11:47404083-47440081	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
9	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10838703	C1QTNF4	cis	lymphoblastoid	seeQTL
rs10838703	SPI1	cis	multi-tissue	Pritchard
rs10838703	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10838703	OR4B1	cis	cerebellum	SCAN
rs10838703	MADD	cis	parietal	SCAN
rs10838703	SLC39A13	cis	cerebellum	SCAN
rs10838703	MADD	cis	Esophagus Muscularis	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47420000-47423400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr11:47421200-47423000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr11:47421200-47423200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr11:47421200-47423200	Enhancers	Fetal Heart	heart
5	chr11:47421200-47423400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:47422000-47423000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr11:47422000-47423000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr11:47422000-47423000	Flanking Active TSS	GM12878-XiMat	blood
9	chr11:47422200-47423000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:47422200-47423000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr11:47422200-47423000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr11:47422200-47423000	Enhancers	Liver	Liver
13	chr11:47422200-47423000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:47422200-47423400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr11:47422200-47423600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:47422200-47428800	Weak transcription	NH-A	brain
17	chr11:47422400-47423000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr11:47422400-47423000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:47422400-47423000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr11:47422400-47423000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr11:47422400-47423200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr11:47422400-47423200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr11:47422400-47423400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:47422400-47423400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:47422400-47423600	Enhancers	Primary B cells from peripheral blood	blood
26	chr11:47422400-47423800	Enhancers	Primary hematopoietic stem cells	blood
27	chr11:47422400-47423800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr11:47422400-47428800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr11:47422400-47429000	Weak transcription	Fetal Brain Female	brain
30	chr11:47422600-47423000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr11:47422600-47423000	Enhancers	H9 Cell Line	embryonic stem cell
32	chr11:47422600-47423000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr11:47422600-47423000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr11:47422600-47423000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:47422600-47423000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:47422600-47423000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr11:47422600-47423000	Enhancers	Brain Substantia Nigra	brain
38	chr11:47422600-47423000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr11:47422600-47423000	Enhancers	Hela-S3	cervix
40	chr11:47422600-47423200	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr11:47422600-47423400	Enhancers	K562	blood
42	chr11:47422600-47423600	Weak transcription	Gastric	stomach
43	chr11:47422600-47423800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:47422600-47424600	Weak transcription	HepG2	liver
45	chr11:47422600-47429000	Weak transcription	HSMMtube	muscle
46	chr11:47422800-47423000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr11:47422800-47423000	Enhancers	Primary T cells from cord blood	blood
48	chr11:47422800-47423000	Enhancers	Brain Anterior Caudate	brain
49	chr11:47422800-47423600	Enhancers	Primary B cells from cord blood	blood
50	chr11:47422800-47423800	Weak transcription	Brain Hippocampus Middle	brain

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