Variant report

Variant	rs11231628
Chromosome Location	chr11:63647524-63647525
allele	A/C
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:0)
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	chr11:63640265..63644644-chr11:63645471..63647891,3	MCF-7	breast:
2	chr11:63603344..63615182-chr11:63634321..63647771,46	MCF-7	breast:
3	chr11:63606304..63609239-chr11:63647374..63650317,2	MCF-7	breast:
4	chr11:63643541..63645532-chr11:63647100..63648960,2	K562	blood:
5	chr11:63646076..63648467-chr11:63649897..63652105,4	K562	blood:
6	chr11:63640055..63641967-chr11:63645955..63648336,2	K562	blood:
7	chr11:63637157..63639514-chr11:63645420..63648152,2	K562	blood:
8	chr11:63646755..63648414-chr11:63654081..63656532,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202089	Chromatin interaction
ENSG00000072518	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10736731	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10751001	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10792421	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10792422	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10792423	0.91[ASN][1000 genomes]
rs10897452	0.87[ASN][1000 genomes]
rs10897453	0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10897454	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10897456	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10897459	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10897465	0.81[CEU][hapmap]
rs11231600	1.00[JPT][hapmap]
rs11231623	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11231640	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11231643	0.87[EUR][1000 genomes]
rs11231646	0.88[TSI][hapmap]
rs11231662	0.92[CEU][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs11231664	0.92[CEU][hapmap]
rs11231670	0.92[CEU][hapmap]
rs11231671	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs11605500	0.90[ASN][1000 genomes]
rs11605797	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs12277481	0.91[ASN][1000 genomes]
rs12417507	0.80[EUR][1000 genomes]
rs12421757	0.80[EUR][1000 genomes]
rs12576275	0.92[ASN][1000 genomes]
rs12786124	1.00[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs12792726	0.92[EUR][1000 genomes]
rs12793201	0.87[EUR][1000 genomes]
rs12794404	0.86[EUR][1000 genomes]
rs12797540	0.80[EUR][1000 genomes]
rs12800703	0.87[CEU][hapmap]
rs1872772	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs224173	0.97[EUR][1000 genomes]
rs2318126	1.00[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2840079	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs3019785	0.96[EUR][1000 genomes]
rs3740637	0.88[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs3802941	0.86[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs3850943	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs449047	1.00[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs454474	1.00[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs492357	0.89[CEU][hapmap]
rs4963433	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4980499	0.92[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4980500	0.92[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4980503	0.90[ASN][1000 genomes]
rs4980505	0.95[ASN][1000 genomes]
rs4980507	0.95[ASN][1000 genomes]
rs4980528	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4980529	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4980530	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4980532	0.90[ASN][1000 genomes]
rs4980533	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs504060	0.89[CEU][hapmap]
rs509701	0.88[CEU][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs61604723	0.82[ASN][1000 genomes]
rs61886128	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6591825	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7102006	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7108375	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7110843	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7118913	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7928919	0.88[EUR][1000 genomes]
rs7937314	0.92[ASN][1000 genomes]
rs7939416	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7944519	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7948656	0.87[ASN][1000 genomes]
rs923247	0.95[ASN][1000 genomes]
rs928948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1839119	chr11:63615554-63680052	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11231628	ZBTB3	cis	parietal	SCAN
rs11231628	NAALADL1	cis	cerebellum	SCAN
rs11231628	SLC22A8	cis	parietal	SCAN
rs11231628	FADS2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63637800-63653200	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr11:63640000-63647800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:63641000-63654800	Weak transcription	HepG2	liver
4	chr11:63642200-63654800	Weak transcription	Fetal Lung	lung
5	chr11:63642400-63654400	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:63642400-63655000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:63642800-63648000	Enhancers	Brain Hippocampus Middle	brain
8	chr11:63643000-63648000	Enhancers	Brain Anterior Caudate	brain
9	chr11:63643600-63655800	Weak transcription	Aorta	Aorta
10	chr11:63643800-63652400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr11:63644000-63650400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:63644400-63648200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr11:63644400-63648800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr11:63644400-63650200	Weak transcription	GM12878-XiMat	blood
15	chr11:63644600-63655200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr11:63645000-63649400	Enhancers	Brain Cingulate Gyrus	brain
17	chr11:63645000-63652400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr11:63645200-63648200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr11:63645200-63648200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:63645200-63648400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:63645200-63649200	Enhancers	Brain Angular Gyrus	brain
22	chr11:63645400-63647600	Genic enhancers	Fetal Intestine Small	intestine
23	chr11:63645400-63649000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:63645400-63649000	Enhancers	Stomach Mucosa	stomach
25	chr11:63645800-63654600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr11:63646000-63648400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr11:63646200-63648200	Enhancers	H9 Cell Line	embryonic stem cell
28	chr11:63646200-63648200	Enhancers	HMEC	breast
29	chr11:63646200-63648400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:63646200-63648400	Strong transcription	Primary B cells from cord blood	blood
31	chr11:63646200-63648400	Genic enhancers	Primary T cells from cord blood	blood
32	chr11:63646200-63648400	Enhancers	NHDF-Ad	bronchial
33	chr11:63646200-63648400	Enhancers	Osteobl	bone
34	chr11:63646200-63650800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:63646400-63648000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr11:63646400-63648000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:63646400-63648200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:63646400-63652200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr11:63646600-63647600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr11:63646600-63647800	Enhancers	Fetal Intestine Large	intestine
41	chr11:63646600-63652000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr11:63646600-63652600	Enhancers	Fetal Thymus	thymus
43	chr11:63646800-63647600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:63646800-63647600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:63646800-63647600	Enhancers	Liver	Liver
46	chr11:63646800-63647800	Enhancers	Small Intestine	intestine
47	chr11:63646800-63648000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr11:63646800-63648000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:63646800-63648000	Enhancers	A549	lung
50	chr11:63646800-63648200	Enhancers	HUES6 Cell Line	embryonic stem cell

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