Variant report

Variant	rs9461317
Chromosome Location	chr6:26988919-26988920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26986672..26989789-chr6:27000178..27003902,5	K562	blood:
2	chr6:26987473..26989344-chr6:26998770..27002540,3	MCF-7	breast:
3	chr6:26986141..26989315-chr6:27099693..27102722,3	K562	blood:
4	chr6:26596362..26598030-chr6:26986586..26989465,2	MCF-7	breast:
5	chr6:26923074..26925467-chr6:26986570..26988926,2	K562	blood:
6	chr6:26987456..26989789-chr6:27000178..27002693,2	K562	blood:
7	chr6:26595477..26598975-chr6:26986599..26989051,3	K562	blood:
8	chr6:26987953..26990006-chr6:27113419..27115152,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIST1H2AG-3	chr6:26988232-26991804	NONHSAT108325
2	lnc-HIST1H2BJ-8	chr6:26985858-26989416	NONHSAT108322

No data

Variant related genes	Relation type
ENSG00000196787	Chromatin interaction
ENSG00000224843	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000241549	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000220581	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12180063	0.87[ASN][1000 genomes]
rs12182179	0.87[ASN][1000 genomes]
rs2008668	1.00[ASN][1000 genomes]
rs2754597	1.00[ASN][1000 genomes]
rs35741362	0.94[ASN][1000 genomes]
rs4602717	1.00[ASN][1000 genomes]
rs56853796	0.87[ASN][1000 genomes]
rs59281843	0.87[ASN][1000 genomes]
rs6904523	0.94[ASN][1000 genomes]
rs6913271	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6920796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6929114	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6931748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6932003	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7739691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7751878	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7763149	0.87[ASN][1000 genomes]
rs858983	1.00[JPT][hapmap]
rs9295729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9357029	1.00[ASN][1000 genomes]
rs9368487	1.00[ASN][1000 genomes]
rs9461305	0.87[ASN][1000 genomes]
rs9461318	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461329	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9467927	0.87[ASN][1000 genomes]
rs9467928	0.87[ASN][1000 genomes]
rs9467934	1.00[ASN][1000 genomes]
rs9467947	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467973	1.00[ASN][1000 genomes]
rs9885950	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	esv2758038	chr6:26695219-27095714	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
3	esv2759410	chr6:26695219-27095714	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
4	nsv1029124	chr6:26825468-27109774	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	244 gene(s)	inside rSNPs	diseases
5	nsv469610	chr6:26841083-26999230	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv482509	chr6:26841083-26999230	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv471636	chr6:26841084-27038175	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv469675	chr6:26848950-27015598	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv482429	chr6:26848950-27015598	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv830616	chr6:26859097-27030476	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	esv1810582	chr6:26889428-26990246	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv469625	chr6:26893739-27038175	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv482537	chr6:26893739-27038175	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26987000-26989000	Active TSS	Fetal Kidney	kidney
2	chr6:26987000-26990200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:26987200-26989000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:26988200-26989000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
5	chr6:26988200-26989000	Flanking Active TSS	K562	blood
6	chr6:26988400-26989000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
7	chr6:26988400-26989200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr6:26988400-26990800	Weak transcription	Ovary	ovary
9	chr6:26988600-26989000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr6:26988600-26989000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:26988600-26989000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:26988600-26989000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:26988600-26989000	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr6:26988600-26989000	Active TSS	GM12878-XiMat	blood
15	chr6:26988600-26989200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:26988600-26989200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr6:26988600-26989200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
18	chr6:26988600-26989200	Active TSS	HMEC	breast
19	chr6:26988600-26991600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:26988600-26992800	Weak transcription	Pancreas	Pancrea
21	chr6:26988600-26993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:26988800-26989000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr6:26988800-26989000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:26988800-26989000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr6:26988800-26989000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:26988800-26989000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
27	chr6:26988800-26989200	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links