Variant report

Variant	rs7759217
Chromosome Location	chr6:27730463-27730464
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:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27598999..27601742-chr6:27728041..27730837,2	K562	blood:
2	chr6:27720750..27725347-chr6:27727186..27730834,4	MCF-7	breast:
3	chr6:27342508..27344098-chr6:27729808..27732720,2	K562	blood:
4	chr6:27729351..27732298-chr6:27734296..27736839,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIST1H2AI-1	chr6:27729504-27730863	XLOC_005221
2	lnc-HIST1H2AI-1	chr6:27730299-27730966	NONHSAT108404

No data

Variant related genes	Relation type
ENSG00000238648	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10214440	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10484401	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1139226	0.83[EUR][1000 genomes]
rs13211701	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13215072	0.83[EUR][1000 genomes]
rs169262	0.92[ASN][1000 genomes]
rs1985099	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200468	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs200474	0.91[ASN][1000 genomes]
rs200475	0.93[ASN][1000 genomes]
rs200476	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs200502	0.86[CEU][hapmap]
rs200994	0.84[CHD][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap]
rs2056925	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2092075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179094	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2179095	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2394000	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2394002	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893929	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893930	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2893931	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34752872	0.91[EUR][1000 genomes]
rs35069907	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35957409	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4140646	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711163	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713118	0.83[EUR][1000 genomes]
rs4713121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6901520	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6902689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6914924	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6922574	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6930992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs742046	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742047	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs760587	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7756968	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7760523	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7772027	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7773070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776351	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9283880	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9283881	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9283882	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9283883	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295740	0.87[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs9295742	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295743	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295746	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9295747	0.83[TSI][hapmap]
rs9348774	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs9348775	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9357045	0.81[ASN][1000 genomes]
rs9366700	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9366702	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368528	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9368529	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9368530	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380010	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9380011	0.91[EUR][1000 genomes]
rs9380012	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393847	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393848	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461401	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9461406	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9468195	0.83[EUR][1000 genomes]
rs9468200	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468201	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468203	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468204	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468206	0.95[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468214	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468217	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9468219	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468220	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468229	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7759217	AL022393.7	cis	Muscle Skeletal	GTEx
rs7759217	HIST1H2BM	cis	cerebellum	SCAN
rs7759217	HIST1H3C	cis	cerebellum	SCAN
rs7759217	HIST1H3D	cis	parietal	SCAN
rs7759217	ZKSCAN3	cis	parietal	SCAN
rs7759217	BTN3A3	cis	parietal	SCAN
rs7759217	OR2B8P	cis	Thyroid	GTEx
rs7759217	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs7759217	ZNF204P	cis	parietal	SCAN
rs7759217	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs7759217	BTN3A3	cis	cerebellum	SCAN
rs7759217	BTN2A1	cis	parietal	SCAN
rs7759217	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
2	chr6:27726400-27733000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:27726400-27738600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:27729200-27730600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
5	chr6:27729200-27730800	Active TSS	Primary B cells from cord blood	blood
6	chr6:27729200-27730800	Active TSS	Primary T cells from cord blood	blood
7	chr6:27729200-27731000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:27729400-27730600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:27729400-27730600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:27729400-27730600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
11	chr6:27729400-27730600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
12	chr6:27729400-27730600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
13	chr6:27729400-27730600	Active TSS	Placenta Amnion	Placenta Amnion
14	chr6:27729400-27730600	Active TSS	Thymus	Thymus
15	chr6:27729400-27730800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr6:27729400-27730800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:27729600-27730800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:27729600-27731000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:27729600-27732600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:27729600-27737000	Weak transcription	K562	blood
21	chr6:27729800-27730800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:27729800-27730800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:27729800-27730800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:27730000-27730800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
25	chr6:27730000-27730800	Bivalent/Poised TSS	Right Ventricle	heart
26	chr6:27730000-27731000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:27730200-27730600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:27730200-27730600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
29	chr6:27730200-27730600	Flanking Active TSS	Fetal Heart	heart
30	chr6:27730200-27730600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
31	chr6:27730200-27730600	ZNF genes & repeats	Spleen	Spleen
32	chr6:27730200-27730600	Active TSS	NHEK	skin
33	chr6:27730200-27730800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
34	chr6:27730200-27730800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
35	chr6:27730200-27730800	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr6:27730200-27730800	Strong transcription	Fetal Intestine Small	intestine
37	chr6:27730400-27730600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:27730400-27730600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:27730400-27730600	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:27730400-27730600	Bivalent Enhancer	Left Ventricle	heart
41	chr6:27730400-27730600	Flanking Active TSS	NH-A	brain
42	chr6:27730400-27731000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links