Variant report

Variant	rs1038101
Chromosome Location	chr11:27385939-27385940
allele	A/G
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	E2F4	chr11:27385894-27386094	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr11:27383051-27386155	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr11:27385623-27386108	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr11:27385887-27387063	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:27384214-27387108	A549	lung:	n/a	n/a
6	POLR2A	chr11:27382996-27386830	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:27383389..27386208-chr11:27406370..27407879,2	K562	blood:
2	chr11:27383589..27390199-chr11:27492927..27496354,6	MCF-7	breast:
3	chr11:27374255..27376525-chr11:27385818..27387748,2	K562	blood:

Variant related genes	Relation type
CCDC34	TF binding region
ENSG00000254862	Chromatin interaction
ENSG00000205213	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs35107435	1.00[AFR][1000 genomes]
rs61887480	1.00[AFR][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	nsv467782	chr11:27192715-27496161	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv553914	chr11:27192715-27496161	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1038101	LGR4	Cis_1M	lymphoblastoid	RTeQTL
rs1038101	C11orf46	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:27385000-27403400	Weak transcription	Spleen	Spleen
2	chr11:27385000-27412200	Weak transcription	Small Intestine	intestine
3	chr11:27385200-27408000	Weak transcription	Lung	lung
4	chr11:27385200-27417800	Weak transcription	Gastric	stomach
5	chr11:27385400-27386200	Enhancers	Liver	Liver
6	chr11:27385400-27388800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:27385400-27389200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:27385400-27389200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:27385400-27389200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:27385400-27389200	Weak transcription	Ovary	ovary
11	chr11:27385400-27389200	Weak transcription	HSMMtube	muscle
12	chr11:27385400-27389400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:27385400-27389400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:27385400-27389400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:27385400-27389400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:27385400-27389400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:27385400-27389400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:27385400-27389400	Weak transcription	Aorta	Aorta
19	chr11:27385400-27389400	Weak transcription	Esophagus	oesophagus
20	chr11:27385400-27389400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr11:27385400-27389400	Weak transcription	Left Ventricle	heart
22	chr11:27385400-27389400	Weak transcription	Pancreas	Pancrea
23	chr11:27385400-27391400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:27385400-27391400	Weak transcription	NHLF	lung
25	chr11:27385400-27393000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr11:27385400-27393400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:27385400-27400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:27385400-27400400	Weak transcription	Psoas Muscle	Psoas
29	chr11:27385400-27400600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:27385400-27406600	Weak transcription	Brain Hippocampus Middle	brain
31	chr11:27385400-27407000	Weak transcription	Right Ventricle	heart
32	chr11:27385400-27418600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:27385600-27386000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr11:27385600-27386000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr11:27385600-27386000	Enhancers	Fetal Kidney	kidney
36	chr11:27385600-27386000	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr11:27385600-27386200	Enhancers	Dnd41	blood
38	chr11:27385600-27386200	Enhancers	NHEK	skin
39	chr11:27385600-27386600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:27385600-27388200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:27385600-27388400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:27385600-27388400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr11:27385600-27388600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:27385600-27388600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:27385600-27388800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:27385600-27388800	Weak transcription	Hela-S3	cervix
47	chr11:27385600-27389000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr11:27385600-27389000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr11:27385600-27389000	Weak transcription	NH-A	brain
50	chr11:27385600-27389200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links