Variant report

Variant	rs7944519
Chromosome Location	chr11:63617324-63617325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63610591..63619595-chr11:63634759..63639809,13	MCF-7	breast:
2	chr11:63605094..63609854-chr11:63611414..63617957,11	K562	blood:

Variant related genes	Relation type
ENSG00000072518	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10736731	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10751001	0.93[ASN][1000 genomes]
rs10792421	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10792422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792423	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10897452	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10897453	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10897454	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[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231600	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11231606	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231624	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11231628	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11231637	1.00[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs11231640	0.93[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11231646	0.80[CHB][hapmap]
rs11605500	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12277481	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12576275	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1486936	1.00[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs1872772	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840079	0.93[ASW][hapmap];0.89[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs320109	1.00[CEU][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs3802941	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3850943	0.93[ASN][1000 genomes]
rs4143327	0.91[EUR][1000 genomes]
rs4963433	0.93[ASN][1000 genomes]
rs4980503	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4980505	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4980507	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4980528	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4980529	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4980532	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4980533	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61604723	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6421686	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591825	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7102006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7105288	1.00[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs7108375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7110843	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7118913	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7121067	0.85[EUR][1000 genomes]
rs72934134	0.83[AFR][1000 genomes]
rs7937314	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7939351	0.87[EUR][1000 genomes]
rs7939416	0.88[ASN][1000 genomes]
rs7946503	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7948656	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs923247	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs928948	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7944519	DPF2	cis	parietal	SCAN
rs7944519	NAALADL1	cis	cerebellum	SCAN
rs7944519	ZBTB3	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63608400-63618600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:63609400-63618400	Weak transcription	Ovary	ovary
3	chr11:63609600-63619200	Weak transcription	HSMMtube	muscle
4	chr11:63609600-63629600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:63610200-63633200	Weak transcription	Fetal Brain Male	brain
6	chr11:63611000-63620200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:63611800-63617400	Strong transcription	Fetal Stomach	stomach
8	chr11:63611800-63629800	Weak transcription	Aorta	Aorta
9	chr11:63612000-63618000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:63612600-63618400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:63613000-63618400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:63613000-63618600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:63613000-63622600	Weak transcription	Brain Germinal Matrix	brain
14	chr11:63613200-63625600	Weak transcription	HUVEC	blood vessel
15	chr11:63613200-63626200	Weak transcription	NHLF	lung
16	chr11:63613200-63632400	Weak transcription	Fetal Brain Female	brain
17	chr11:63613200-63633000	Weak transcription	HSMM	muscle
18	chr11:63613400-63618200	Weak transcription	Primary B cells from cord blood	blood
19	chr11:63613400-63618200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:63613400-63618600	Weak transcription	Osteobl	bone
21	chr11:63613400-63619000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:63613400-63619000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:63613600-63618200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr11:63613600-63618400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:63613600-63619000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:63613800-63618200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr11:63613800-63618400	Weak transcription	K562	blood
28	chr11:63613800-63625400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:63614600-63617400	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr11:63614600-63619600	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr11:63614800-63621000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:63615000-63618000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr11:63615000-63618400	Weak transcription	Liver	Liver
34	chr11:63615200-63619000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:63615400-63618000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:63615400-63618200	Weak transcription	A549	lung
37	chr11:63615400-63618400	Weak transcription	Colonic Mucosa	Colon
38	chr11:63615400-63618400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr11:63615400-63618600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:63615600-63617400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:63615600-63618000	Weak transcription	HepG2	liver
42	chr11:63615600-63618200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:63615600-63618200	Weak transcription	Gastric	stomach
44	chr11:63615600-63618200	Weak transcription	Small Intestine	intestine
45	chr11:63615600-63618400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:63615600-63618400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:63615600-63618400	Weak transcription	Psoas Muscle	Psoas
48	chr11:63615600-63618400	Weak transcription	Hela-S3	cervix
49	chr11:63615600-63618600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr11:63615600-63619000	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links