Variant report

Variant	rs2010190
Chromosome Location	chr6:24496314-24496315
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:24494836-24496411	GM12891	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24473016..24474847-chr6:24495882..24498664,2	K562	blood:
2	chr6:24493014..24496474-chr6:24718971..24722650,4	K562	blood:
3	chr6:24495510..24496378-chr6:24695478..24696466,2	MCF-7	breast:
4	chr6:24487824..24490266-chr6:24492770..24497111,3	MCF-7	breast:
5	chr6:24494650..24496587-chr6:24665440..24668079,2	MCF-7	breast:
6	chr6:24488265..24492557-chr6:24493494..24498787,7	K562	blood:
7	chr6:24401784..24404907-chr6:24494976..24497958,4	MCF-7	breast:
8	chr6:24494081..24496615-chr6:24665704..24668263,2	K562	blood:
9	chr6:24494955..24497307-chr6:24719219..24721474,2	MCF-7	breast:
10	chr6:24483355..24485478-chr6:24495554..24497195,2	MCF-7	breast:
11	chr6:24495596..24498223-chr6:24565020..24567302,2	MCF-7	breast:
12	chr6:24495638..24500234-chr6:24504925..24509115,5	K562	blood:

No data

Variant related genes	Relation type
GPLD1	TF binding region
ENSG00000112293	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000124532	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000112304	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1569579	0.82[CHB][hapmap]
rs2744551	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2744554	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2744555	0.85[ASN][1000 genomes]
rs2744572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744582	0.91[ASN][1000 genomes]
rs2744588	0.88[ASN][1000 genomes]
rs2760137	0.88[ASN][1000 genomes]
rs2760138	0.83[CHB][hapmap]
rs2760146	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760153	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793445	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817204	0.94[ASN][1000 genomes]
rs2817215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2817217	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817218	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817226	0.88[ASN][1000 genomes]
rs2817227	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817231	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2817247	0.90[ASN][1000 genomes]
rs2817248	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs941437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv519552	chr6:24451256-24524704	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv883480	chr6:24481299-24507519	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3351586	chr6:24494123-24497171	Bivalent/Poised TSS Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24494800-24496400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:24494800-24496600	Active TSS	Brain Cingulate Gyrus	brain
3	chr6:24495000-24496400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:24495400-24496600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr6:24495400-24496600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:24495600-24496400	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr6:24495600-24496600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:24495600-24496600	Flanking Active TSS	Dnd41	blood
9	chr6:24495800-24496400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:24495800-24496400	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr6:24495800-24496600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:24495800-24517800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:24496000-24496400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr6:24496000-24496400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:24496000-24496400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr6:24496000-24496600	Enhancers	Primary B cells from peripheral blood	blood
17	chr6:24496000-24496600	Enhancers	Fetal Brain Male	brain
18	chr6:24496000-24496600	Enhancers	Placenta	Placenta
19	chr6:24496000-24496600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr6:24496000-24496800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:24496000-24496800	Flanking Active TSS	Liver	Liver
22	chr6:24496000-24496800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:24496000-24501600	Weak transcription	A549	lung
24	chr6:24496000-24513000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:24496000-24517800	Weak transcription	Spleen	Spleen
26	chr6:24496000-24534200	Weak transcription	Gastric	stomach
27	chr6:24496000-24538000	Weak transcription	Esophagus	oesophagus
28	chr6:24496200-24496400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
29	chr6:24496200-24496400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
30	chr6:24496200-24496400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:24496200-24496400	Enhancers	Primary B cells from cord blood	blood
32	chr6:24496200-24496400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:24496200-24496400	Weak transcription	Brain Anterior Caudate	brain
34	chr6:24496200-24496400	Active TSS	Brain Germinal Matrix	brain
35	chr6:24496200-24496400	Enhancers	Colon Smooth Muscle	Colon
36	chr6:24496200-24496400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr6:24496200-24496400	Enhancers	Fetal Kidney	kidney
38	chr6:24496200-24496400	Enhancers	Fetal Muscle Leg	muscle
39	chr6:24496200-24496400	Enhancers	Fetal Stomach	stomach
40	chr6:24496200-24496400	Enhancers	Fetal Thymus	thymus
41	chr6:24496200-24496400	Weak transcription	Left Ventricle	heart
42	chr6:24496200-24496400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr6:24496200-24496400	Enhancers	Thymus	Thymus
44	chr6:24496200-24496400	Weak transcription	K562	blood
45	chr6:24496200-24496600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
46	chr6:24496200-24496600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr6:24496200-24496600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr6:24496200-24496600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:24496200-24496600	Active TSS	Brain Angular Gyrus	brain
50	chr6:24496200-24496600	Enhancers	Duodenum Mucosa	Duodenum

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