Variant report

Variant	rs4938871
Chromosome Location	chr11:57329402-57329403
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57224656..57225281-chr11:57329063..57329842,2	K562	blood:
2	chr11:57327395..57330441-chr11:57334291..57337676,3	K562	blood:
3	chr11:57327644..57330005-chr11:57333922..57337612,3	MCF-7	breast:
4	chr11:57258661..57259261-chr11:57328962..57329548,2	MCF-7	breast:
5	chr11:57297426..57300384-chr11:57328449..57331684,3	K562	blood:
6	chr11:57328509..57330286-chr11:57332816..57335358,2	K562	blood:

Variant related genes	Relation type
ENSG00000134809	Chromatin interaction
ENSG00000156587	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10792101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10792104	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792107	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896629	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1115172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11229057	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508443	0.82[CHB][hapmap]
rs28362945	0.80[ASN][1000 genomes]
rs3891975	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4938873	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939149	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4939151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4939152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939153	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61886733	0.92[ASN][1000 genomes]
rs61886736	0.92[ASN][1000 genomes]
rs61887019	0.92[ASN][1000 genomes]
rs7101425	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7112126	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128015	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131076	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940223	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950126	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1051032	chr11:57290124-57363064	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541049	chr11:57290124-57363064	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1052073	chr11:57297499-57362802	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv541050	chr11:57297499-57362802	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4938871	OR5J2	cis	parietal	SCAN
rs4938871	TIMM10	cis	multi-tissue	Pritchard
rs4938871	TIMM10	trans	brain	seeQTL
rs4938871	SMTNL1	cis	Artery Tibial	GTEx
rs4938871	TIMM10	cis	brain	seeQTL
rs4938871	CLP1	cis	cerebellum	SCAN
rs4938871	TIMM10	cis	lung	GTEx
rs4938871	SERPING1	cis	cerebellum	SCAN
rs4938871	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs4938871	TIMM10	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
2	chr11:57307200-57333600	Weak transcription	HMEC	breast
3	chr11:57309200-57333400	Weak transcription	Psoas Muscle	Psoas
4	chr11:57313200-57330000	Strong transcription	Dnd41	blood
5	chr11:57314000-57330200	Strong transcription	Fetal Intestine Small	intestine
6	chr11:57314000-57330400	Strong transcription	Primary T cells from cord blood	blood
7	chr11:57314200-57329800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr11:57314800-57330600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:57315000-57330000	Weak transcription	NHEK	skin
10	chr11:57315200-57329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:57315200-57329600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:57315200-57330600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:57315600-57330600	Strong transcription	Fetal Muscle Leg	muscle
14	chr11:57315800-57330000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:57315800-57330200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:57315800-57330800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:57320600-57329600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:57320600-57333400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:57320600-57334800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:57320800-57332800	Weak transcription	Stomach Mucosa	stomach
21	chr11:57321000-57333400	Weak transcription	HepG2	liver
22	chr11:57322000-57329800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:57322000-57334600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:57322200-57329800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:57322200-57333200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr11:57322200-57333400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:57322200-57333400	Weak transcription	HSMMtube	muscle
28	chr11:57322200-57333600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:57322200-57333600	Weak transcription	Right Ventricle	heart
30	chr11:57322800-57333400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:57323000-57333200	Weak transcription	NHDF-Ad	bronchial
32	chr11:57323800-57333800	Weak transcription	Aorta	Aorta
33	chr11:57324000-57334000	Weak transcription	Pancreas	Pancrea
34	chr11:57324400-57333800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr11:57324800-57332800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr11:57324800-57333200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:57326400-57332800	Weak transcription	Brain Substantia Nigra	brain
38	chr11:57326400-57333600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:57326600-57329800	Weak transcription	Left Ventricle	heart
40	chr11:57326600-57332800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:57326600-57332800	Weak transcription	Brain Anterior Caudate	brain
42	chr11:57326600-57333200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr11:57326600-57333200	Weak transcription	Fetal Lung	lung
44	chr11:57326600-57333400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:57326600-57333400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:57326800-57330200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:57326800-57330400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:57326800-57332800	Weak transcription	Colonic Mucosa	Colon
49	chr11:57326800-57332800	Weak transcription	Thymus	Thymus
50	chr11:57326800-57333000	Weak transcription	Brain Inferior Temporal Lobe	brain

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