Variant report

Variant	rs1109527
Chromosome Location	chr5:52387150-52387151
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:52387080-52387230	HA-sp	spinal cord:	n/a	n/a
2	CTCF	chr5:52387040-52387190	MCF-7	breast:	n/a	n/a
3	CTCF	chr5:52387040-52387190	NHDF-neo	bronchial:	n/a	n/a
4	CTCF	chr5:52387000-52387150	BJ	skin:	n/a	n/a
5	POLR2A	chr5:52387034-52387323	Hela-S3	cervix:	n/a	n/a
6	RAD21	chr5:52387108-52387445	IMR90	lung:	n/a	n/a
7	POLR2A	chr5:52387095-52388026	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr5:52387040-52387190	BJ	skin:	n/a	n/a
9	NFIC	chr5:52387092-52387740	SK-N-SH	brain:	n/a	n/a
10	FOSL2	chr5:52387080-52387517	A549	lung:	n/a	n/a
11	CTCF	chr5:52387020-52387540	IMR90	lung:	n/a	n/a
12	CTCF	chr5:52387060-52387210	HCFaa	heart:	n/a	n/a
13	CTCF	chr5:52387115-52387183	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr5:52387060-52387210	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr5:52387040-52387190	BE2_C	brain:	n/a	n/a
16	JUND	chr5:52386991-52387613	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:52282305..52286125-chr5:52387011..52391029,5	MCF-7	breast:
2	chr5:52384729..52387843-chr5:52404184..52407459,4	MCF-7	breast:
3	chr5:52386358..52388185-chr5:52389009..52390618,2	MCF-7	breast:
4	chr5:52385620..52387718-chr5:52408236..52410843,2	MCF-7	breast:
5	chr5:52246465..52248425-chr5:52385773..52388530,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272123	TF binding region
ENSG00000164172	Chromatin interaction
ENSG00000249899	Chromatin interaction
ENSG00000247796	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1421934	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs152089	0.88[CEU][hapmap]
rs1541689	0.91[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs1549276	0.81[CHB][hapmap];0.94[YRI][hapmap]
rs1833557	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2287872	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406599	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs25826	0.86[EUR][1000 genomes]
rs27406	0.92[EUR][1000 genomes]
rs27420	0.88[EUR][1000 genomes]
rs27915	0.90[MKK][hapmap];0.81[YRI][hapmap]
rs30099	0.81[ASW][hapmap];0.88[CEU][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs30727	0.92[EUR][1000 genomes]
rs3212616	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7719848	0.94[YRI][hapmap]
rs996765	0.93[AFR][1000 genomes];0.94[EUR][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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:52341200-52396400	Strong transcription	HMEC	breast
5	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
7	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
8	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
11	chr5:52360200-52388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
13	chr5:52362200-52387800	Strong transcription	HepG2	liver
14	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
15	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
19	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
20	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:52372200-52392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:52372200-52394800	Weak transcription	Gastric	stomach
23	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
24	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:52374200-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:52379200-52388400	Strong transcription	Hela-S3	cervix
28	chr5:52380000-52391200	Weak transcription	Fetal Brain Female	brain
29	chr5:52381200-52394200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:52382800-52395000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:52383000-52390800	Weak transcription	Fetal Heart	heart
32	chr5:52383000-52393000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:52383000-52394800	Weak transcription	Brain Anterior Caudate	brain
34	chr5:52383200-52394800	Weak transcription	Esophagus	oesophagus
35	chr5:52383200-52394800	Weak transcription	Spleen	Spleen
36	chr5:52383800-52389000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr5:52383800-52392200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:52383800-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:52383800-52395000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:52384000-52387400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:52384000-52387400	Weak transcription	Fetal Intestine Large	intestine
42	chr5:52384000-52387400	Weak transcription	Lung	lung
43	chr5:52384000-52394600	Weak transcription	Brain Angular Gyrus	brain
44	chr5:52384000-52394800	Weak transcription	Brain Substantia Nigra	brain
45	chr5:52384000-52395200	Weak transcription	Brain Hippocampus Middle	brain
46	chr5:52384200-52394800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:52384400-52387200	Weak transcription	Fetal Muscle Leg	muscle
48	chr5:52384400-52392800	Weak transcription	Fetal Intestine Small	intestine
49	chr5:52384600-52388400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:52385200-52389800	Strong transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links