Variant report

Variant	rs728919
Chromosome Location	chr11:63708574-63708575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63682242..63690244-chr11:63703955..63713214,18	K562	blood:
2	chr11:63683456..63690158-chr11:63704393..63714412,17	K562	blood:
3	chr11:63708040..63711029-chr11:63752724..63754511,2	K562	blood:
4	chr11:63601389..63603149-chr11:63706339..63708895,2	K562	blood:
5	chr11:63708455..63711957-chr11:63724529..63727502,3	K562	blood:
6	chr11:63683018..63687693-chr11:63704987..63708969,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167770	Chromatin interaction
ENSG00000167771	Chromatin interaction
ENSG00000256280	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10751004	0.93[EUR][1000 genomes]
rs10792424	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10897459	0.83[TSI][hapmap]
rs10897464	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]
rs10897466	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs10897468	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11231646	0.93[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11231653	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11231655	0.82[EUR][1000 genomes]
rs11231662	0.81[MEX][hapmap];0.80[TSI][hapmap]
rs11231671	0.80[TSI][hapmap]
rs11601228	0.92[EUR][1000 genomes]
rs11602912	0.86[AFR][1000 genomes]
rs11605797	0.80[TSI][hapmap]
rs11607028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417507	0.83[EUR][1000 genomes]
rs12421757	0.83[EUR][1000 genomes]
rs12786124	0.81[TSI][hapmap]
rs12790749	0.92[EUR][1000 genomes]
rs12797540	0.83[EUR][1000 genomes]
rs12798491	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs12800703	0.80[CEU][hapmap]
rs12808604	0.92[EUR][1000 genomes]
rs1386346	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1684950	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1783964	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2318110	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2508584	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3019782	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs320121	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs320156	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35492216	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3740636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740637	0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4426138	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs480211	0.83[CHB][hapmap]
rs481835	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs483340	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs487540	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs488082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4980499	0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4980500	0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4980509	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4980512	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4980516	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4980530	0.83[TSI][hapmap]
rs499118	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs500493	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs502858	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs504314	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs509701	0.81[MEX][hapmap]
rs528927	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs529915	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs539432	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs540389	0.83[CHB][hapmap]
rs553724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs562865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs567386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs578295	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6591830	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs709594	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7111130	0.85[EUR][1000 genomes]
rs7112348	0.81[EUR][1000 genomes]
rs7928990	0.91[EUR][1000 genomes]
rs7938498	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7942318	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7951529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943682	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv468589	chr11:63515752-63713239	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv555180	chr11:63515752-63713239	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS 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	39 gene(s)	inside rSNPs	diseases
4	nsv468590	chr11:63639881-63783352	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv555181	chr11:63639881-63783352	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv897629	chr11:63664882-63866959	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
9	nsv897639	chr11:63691049-63844683	Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs728919	C11orf95	cis	cerebellum	SCAN
rs728919	BEST1	cis	cerebellum	SCAN
rs728919	TM7SF2	cis	cerebellum	SCAN
rs728919	HRASLS3	cis	multi-tissue	Pritchard
rs728919	B3GNT1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63706400-63708800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:63706600-63708800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:63707000-63708600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr11:63707200-63708600	Enhancers	Spleen	Spleen
5	chr11:63707200-63709000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr11:63707200-63724200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:63707400-63708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:63707400-63708600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr11:63707400-63708600	Enhancers	Fetal Heart	heart
10	chr11:63707400-63708800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr11:63707400-63708800	Enhancers	Brain Angular Gyrus	brain
12	chr11:63707400-63709000	Enhancers	Brain Substantia Nigra	brain
13	chr11:63707400-63709200	Enhancers	Primary B cells from peripheral blood	blood
14	chr11:63707400-63709600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr11:63707400-63710600	Weak transcription	Psoas Muscle	Psoas
16	chr11:63707400-63712400	Weak transcription	Esophagus	oesophagus
17	chr11:63707400-63712400	Weak transcription	Ovary	ovary
18	chr11:63707400-63712400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr11:63707400-63712600	Weak transcription	Aorta	Aorta
20	chr11:63707400-63713400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:63707400-63713800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:63707400-63713800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:63707400-63719600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:63707400-63721400	Weak transcription	Small Intestine	intestine
25	chr11:63707600-63708600	Enhancers	Brain Anterior Caudate	brain
26	chr11:63707600-63708600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:63707600-63708800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr11:63707600-63708800	Enhancers	Brain Cingulate Gyrus	brain
29	chr11:63707600-63708800	Enhancers	Fetal Lung	lung
30	chr11:63707600-63708800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr11:63707600-63709000	Enhancers	Primary hematopoietic stem cells	blood
32	chr11:63707600-63709000	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr11:63707600-63709400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr11:63707600-63709400	Enhancers	Primary B cells from cord blood	blood
35	chr11:63707600-63710200	Weak transcription	Fetal Intestine Large	intestine
36	chr11:63707600-63710200	Weak transcription	Thymus	Thymus
37	chr11:63707600-63710600	Weak transcription	Right Atrium	heart
38	chr11:63707600-63711000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:63707600-63711400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:63707600-63711800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr11:63707600-63711800	Weak transcription	NHLF	lung
42	chr11:63707600-63712000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:63707600-63712400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:63707600-63712400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr11:63707600-63712400	Weak transcription	Liver	Liver
46	chr11:63707600-63712400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:63707600-63712400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:63707600-63712400	Weak transcription	Osteobl	bone
49	chr11:63707600-63712600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:63707600-63713000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links