Variant report

Variant	rs9467703
Chromosome Location	chr6:26318903-26318904
allele	A/G
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26318766..26321158-chr6:26595395..26597187,2	K562	blood:
2	chr6:26318172..26320821-chr6:26533523..26535253,2	K562	blood:
3	chr6:26317341..26319926-chr6:26320589..26323146,3	MCF-7	breast:
4	chr6:26317773..26322423-chr6:26326646..26329657,4	MCF-7	breast:
5	chr6:26318833..26321012-chr6:26555441..26558176,2	K562	blood:
6	chr6:26318345..26320198-chr6:27114858..27116962,2	MCF-7	breast:
7	chr6:26316879..26321021-chr6:26321669..26325366,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIST1H2BI-3	chr6:26318686-26319429	NONHSAT108260

No data

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000220875	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1124999	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1125000	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11756673	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142703	0.81[ASN][1000 genomes]
rs2179152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2393593	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34916901	0.81[ASN][1000 genomes]
rs3999544	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4145910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412192	0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4413606	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6456714	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6899452	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6916289	0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6935954	0.86[MEX][hapmap]
rs6939048	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939589	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6940237	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs766406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs766407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746807	0.81[ASN][1000 genomes]
rs7747133	0.81[ASN][1000 genomes]
rs7748935	0.81[ASN][1000 genomes]
rs7750868	1.00[YRI][hapmap]
rs7771202	1.00[JPT][hapmap]
rs9357004	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs9358915	1.00[JPT][hapmap]
rs9358917	0.84[ASN][1000 genomes]
rs9358919	0.84[ASN][1000 genomes]
rs9366649	0.90[CHD][hapmap];0.91[GIH][hapmap]
rs9379843	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9393690	1.00[JPT][hapmap]
rs9393692	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs9393694	1.00[JPT][hapmap]
rs9393701	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9461242	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
7	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
8	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
9	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases
10	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv525347	chr6:26313348-26322985	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9467703	HIST1H3G	cis	cerebellum	SCAN
rs9467703	HIST1H2BD	cis	multi-tissue	Pritchard
rs9467703	HIST1H4H	cis	multi-tissue	Pritchard
rs9467703	GMNN	cis	parietal	SCAN
rs9467703	HIST1H2AJ	cis	parietal	SCAN
rs9467703	HIST1H4E	cis	multi-tissue	Pritchard
rs9467703	HIST1H3H	cis	parietal	SCAN
rs9467703	HIST1H3C	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26314000-26319600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:26314200-26321800	Weak transcription	NH-A	brain
3	chr6:26314200-26322000	Weak transcription	Right Atrium	heart
4	chr6:26314400-26319800	Weak transcription	NHEK	skin
5	chr6:26314400-26321400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:26314400-26322000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:26314400-26322200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:26314600-26319000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:26314600-26319800	Weak transcription	Dnd41	blood
10	chr6:26318600-26323400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:26318800-26319000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:26318800-26319000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:26318800-26320000	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr6:26318800-26320200	Flanking Active TSS	HepG2	liver
15	chr6:26318800-26320200	Flanking Active TSS	K562	blood
16	chr6:26318800-26320600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:26318800-26320600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr6:26318800-26320800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:26318800-26321000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr6:26318800-26321200	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:26318800-26323200	Active TSS	H9 Cell Line	embryonic stem cell

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