Variant report

Variant	rs6860504
Chromosome Location	chr5:98267115-98267116
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	CEBPB	chr5:98267066-98267269	HepG2	liver:	n/a	chr5:98267169-98267180 chr5:98267168-98267179 chr5:98267167-98267184 chr5:98267168-98267181
2	TBL1XR1	chr5:98266732-98267460	K562	blood:	n/a	n/a
3	POLR2A	chr5:98262736-98267954	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:98261911-98271717	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr5:98267009-98267291	IMR90	lung:	n/a	chr5:98267169-98267180 chr5:98267168-98267179 chr5:98267167-98267184 chr5:98267168-98267181
6	MAFK	chr5:98266719-98267574	K562	blood:	n/a	chr5:98267070-98267081 chr5:98267069-98267083
7	POLR2A	chr5:98262744-98270017	GM12891	blood:	n/a	n/a
8	RCOR1	chr5:98266632-98267191	K562	blood:	n/a	n/a
9	ZC3H11A	chr5:98266725-98267138	K562	blood:	n/a	n/a
10	RCOR1	chr5:98266742-98267388	K562	blood:	n/a	n/a
11	POLR2A	chr5:98260830-98273878	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:98262437..98267686-chr5:98287585..98292205,9	K562	blood:
2	chr5:90674940..90679357-chr5:98262514..98267275,7	K562	blood:
3	chr5:98265288..98267597-chr5:98314726..98317352,2	K562	blood:
4	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
5	chr5:96142600..96144164-chr5:98264927..98267832,2	K562	blood:
6	chr5:90677652..90679304-chr5:98264702..98267275,2	K562	blood:
7	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:
8	chr5:98265027..98268409-chr5:98365166..98367986,4	K562	blood:
9	chr5:98266485..98269344-chr6:26198000..26199535,2	MCF-7	breast:
10	chr5:98266316..98268754-chr5:98386981..98389928,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGMB-1	chr5:98264861-98270036	NONHSAT102968

Variant related genes	Relation type
CHD1	TF binding region
ENSG00000113369	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000200351	Chromatin interaction
ENSG00000241597	Chromatin interaction
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10069735	0.93[ASN][1000 genomes]
rs161937	0.92[CHD][hapmap]
rs161938	0.84[MKK][hapmap]
rs161941	0.84[MKK][hapmap]
rs161954	0.85[YRI][hapmap]
rs162150	0.85[MKK][hapmap]
rs327811	0.81[YRI][hapmap]
rs692759	0.89[CHD][hapmap]
rs7718898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266000-98268200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:98266000-98269400	Weak transcription	Pancreas	Pancrea
3	chr5:98266000-98269800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:98266000-98271000	Weak transcription	Left Ventricle	heart
5	chr5:98266000-98272400	Weak transcription	Aorta	Aorta
6	chr5:98266000-98276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:98266000-98276400	Weak transcription	Placenta	Placenta
8	chr5:98266200-98267400	Enhancers	Primary T cells from cord blood	blood
9	chr5:98266200-98267400	Enhancers	Fetal Intestine Small	intestine
10	chr5:98266200-98267600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr5:98266200-98268000	Enhancers	Brain Hippocampus Middle	brain
12	chr5:98266200-98268800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:98266200-98269000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr5:98266200-98269400	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr5:98266200-98272600	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:98266200-98273200	Weak transcription	Right Ventricle	heart
17	chr5:98266200-98274200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
19	chr5:98266400-98267200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:98266400-98267200	Enhancers	Fetal Brain Female	brain
21	chr5:98266400-98267400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr5:98266400-98267600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr5:98266400-98267600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:98266400-98268000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:98266400-98269000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr5:98266400-98269200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:98266400-98270400	Weak transcription	HSMMtube	muscle
28	chr5:98266400-98270600	Weak transcription	NH-A	brain
29	chr5:98266400-98270600	Weak transcription	NHLF	lung
30	chr5:98266400-98270800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:98266400-98271000	Weak transcription	Psoas Muscle	Psoas
32	chr5:98266400-98271200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr5:98266400-98271400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr5:98266400-98271400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr5:98266400-98272400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:98266400-98272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:98266400-98273000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:98266400-98273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:98266400-98273400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:98266400-98276200	Weak transcription	Fetal Kidney	kidney
41	chr5:98266600-98267200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr5:98266600-98267200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:98266600-98267200	Enhancers	Brain Anterior Caudate	brain
44	chr5:98266600-98267200	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr5:98266600-98267400	Genic enhancers	Primary B cells from cord blood	blood
46	chr5:98266600-98267400	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr5:98266600-98267400	Enhancers	Brain Substantia Nigra	brain
48	chr5:98266600-98267600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:98266600-98267600	Enhancers	Colon Smooth Muscle	Colon
50	chr5:98266600-98267600	Strong transcription	Fetal Thymus	thymus

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