Variant report

Variant	rs6898518
Chromosome Location	chr5:118789413-118789414
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	GATA1	chr5:118788092-118789851	PBDE	blood:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637
2	POLR2A	chr5:118788062-118790211	HepG2	liver:	n/a	n/a
3	NR2F2	chr5:118788780-118789424	MCF-7	breast:	n/a	n/a
4	POLR2A	chr5:118787604-118790194	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118323861..118326778-chr5:118787539..118789741,2	MCF-7	breast:
2	chr5:118788483..118791355-chr5:118802793..118805177,3	K562	blood:

Variant related genes	Relation type
HSD17B4	TF binding region
ENSG00000169570	Chromatin interaction
ENSG00000239084	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10059654	0.91[EUR][1000 genomes]
rs10463469	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10463711	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11064	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs11738162	0.83[ASN][1000 genomes]
rs11744058	0.85[ASN][1000 genomes]
rs11749784	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs17453681	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs2636966	0.83[ASN][1000 genomes]
rs28943585	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28943586	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756513	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3797371	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs55700001	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55901673	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56349852	0.86[EUR][1000 genomes]
rs72788170	0.85[ASN][1000 genomes]
rs73249978	0.87[EUR][1000 genomes]
rs73249999	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv4974	chr5:118750259-118795376	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS 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	12 gene(s)	inside rSNPs	diseases
4	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118787800-118790000	Active TSS	Fetal Brain Male	brain
2	chr5:118787800-118790200	Active TSS	Aorta	Aorta
3	chr5:118788000-118789600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr5:118788000-118789600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr5:118788000-118789800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr5:118788000-118790000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:118788000-118790000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr5:118788400-118789600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:118788800-118789600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:118788800-118789600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:118788800-118789600	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr5:118788800-118789600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr5:118788800-118789800	Flanking Active TSS	Brain Cingulate Gyrus	brain
14	chr5:118788800-118791000	Flanking Active TSS	Liver	Liver
15	chr5:118789000-118789600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:118789000-118789600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:118789000-118789600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:118789000-118789600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr5:118789000-118789600	Flanking Active TSS	A549	lung
20	chr5:118789000-118789800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr5:118789000-118789800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:118789000-118789800	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr5:118789000-118789800	Flanking Active TSS	Fetal Kidney	kidney
24	chr5:118789000-118789800	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr5:118789000-118790000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:118789000-118790000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:118789000-118790000	Weak transcription	Lung	lung
28	chr5:118789000-118791400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:118789000-118795600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:118789000-118805000	Weak transcription	Esophagus	oesophagus
31	chr5:118789000-118805400	Weak transcription	Ovary	ovary
32	chr5:118789000-118805400	Weak transcription	Spleen	Spleen
33	chr5:118789000-118811800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:118789000-118813200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:118789000-118826800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:118789200-118789600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr5:118789200-118789600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr5:118789200-118789600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:118789200-118789600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr5:118789200-118789600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr5:118789200-118789600	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr5:118789200-118789600	Flanking Active TSS	GM12878-XiMat	blood
43	chr5:118789200-118789800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr5:118789200-118789800	Enhancers	Primary B cells from cord blood	blood
45	chr5:118789200-118789800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr5:118789200-118789800	Enhancers	Fetal Stomach	stomach
47	chr5:118789200-118789800	Enhancers	K562	blood
48	chr5:118789200-118790000	Weak transcription	Left Ventricle	heart
49	chr5:118789200-118790000	Weak transcription	Pancreas	Pancrea
50	chr5:118789200-118790000	Flanking Active TSS	HepG2	liver

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