Variant report

Variant	rs16935599
Chromosome Location	chr11:18636481-18636482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18635208..18638912-chr11:18654317..18656685,3	MCF-7	breast:
2	chr11:18629872..18633193-chr11:18634242..18638507,6	K562	blood:
3	chr11:18635938..18638203-chr11:18650353..18652187,2	MCF-7	breast:
4	chr11:18632328..18634710-chr11:18635963..18638562,2	MCF-7	breast:
5	chr11:18608861..18610567-chr11:18636047..18638073,2	MCF-7	breast:
6	chr11:18602082..18603757-chr11:18635005..18637571,2	MCF-7	breast:
7	chr11:18629851..18633818-chr11:18636242..18638829,5	K562	blood:

Variant related genes	Relation type
ENSG00000151116	Chromatin interaction
ENSG00000179119	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12792924	1.00[CEU][hapmap]
rs12795249	1.00[CEU][hapmap]
rs16935594	0.89[EUR][1000 genomes]
rs34478670	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34637245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35888728	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers 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	144 gene(s)	inside rSNPs	diseases
3	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv516413	chr11:18628418-18643758	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16935599	LDHC	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18612400-18638400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18624000-18637800	Strong transcription	Fetal Muscle Leg	muscle
3	chr11:18624800-18640800	Weak transcription	Right Atrium	heart
4	chr11:18625200-18637200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:18625200-18637800	Strong transcription	A549	lung
6	chr11:18625800-18638400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:18626200-18638000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:18626200-18638800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:18627200-18637200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr11:18627400-18636600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:18627400-18638000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:18627600-18637200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr11:18627600-18637200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:18627600-18637400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:18627600-18637600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr11:18627600-18638200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr11:18627600-18638400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:18628400-18637600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:18628600-18636600	Strong transcription	GM12878-XiMat	blood
20	chr11:18628600-18636800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:18628600-18637200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:18628600-18637600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr11:18628600-18637600	Strong transcription	NH-A	brain
24	chr11:18628600-18638200	Strong transcription	Liver	Liver
25	chr11:18628600-18638200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:18628600-18638400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:18628600-18638600	Strong transcription	Placenta	Placenta
28	chr11:18628800-18637000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:18628800-18637600	Strong transcription	Osteobl	bone
30	chr11:18628800-18637800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr11:18628800-18638400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr11:18629000-18654400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:18629200-18637800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:18629400-18637800	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr11:18629400-18638200	Strong transcription	Dnd41	blood
36	chr11:18629400-18638400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:18629600-18638400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:18629800-18637200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:18629800-18637600	Strong transcription	Primary B cells from cord blood	blood
40	chr11:18629800-18637600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:18629800-18637800	Strong transcription	Thymus	Thymus
42	chr11:18629800-18638000	Strong transcription	Fetal Intestine Large	intestine
43	chr11:18630000-18637000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:18630400-18639800	Weak transcription	Fetal Heart	heart
45	chr11:18630800-18654800	Weak transcription	Psoas Muscle	Psoas
46	chr11:18631000-18637600	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:18631200-18636800	Weak transcription	Hela-S3	cervix
48	chr11:18631600-18636600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr11:18631600-18637600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr11:18633000-18638400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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