Variant report

Variant	rs411279
Chromosome Location	chr8:90808157-90808158
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90774651..90777545-chr8:90807253..90809374,2	MCF-7	breast:
2	chr8:90802147..90804411-chr8:90807957..90809553,2	MCF-7	breast:
3	chr8:90806351..90809015-chr8:90995258..90997957,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104320	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1003843	1.00[ASW][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10095743	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10112852	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13252013	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13252917	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13259882	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13274635	0.89[CEU][hapmap]
rs13279023	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218899	0.91[MEX][hapmap]
rs218902	0.87[MEX][hapmap]
rs218903	0.80[GIH][hapmap]
rs218905	0.88[AMR][1000 genomes]
rs218907	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218908	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218909	0.91[AMR][1000 genomes]
rs218913	0.93[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218914	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218925	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218929	0.93[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218932	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218934	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218936	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs218938	0.89[CEU][hapmap]
rs2644021	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2644033	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2735870	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2735871	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2735873	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2735878	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2735882	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs367640	1.00[YRI][hapmap]
rs369771	0.81[CEU][hapmap]
rs370282	0.89[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs383592	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs385524	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs388866	1.00[YRI][hapmap]
rs394108	0.81[CEU][hapmap];0.84[AMR][1000 genomes]
rs39499	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs39500	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39503	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39504	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39505	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39506	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39508	0.82[CEU][hapmap]
rs39509	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs39515	0.81[CEU][hapmap]
rs397540	0.89[CEU][hapmap]
rs39761	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39763	0.89[CEU][hapmap]
rs39766	0.89[CEU][hapmap]
rs39767	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs400411	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40246	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs40247	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40250	1.00[YRI][hapmap]
rs402886	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40379	0.89[CEU][hapmap]
rs40380	0.85[CEU][hapmap]
rs40381	0.81[EUR][1000 genomes]
rs40382	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs40452	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40454	0.85[CEU][hapmap]
rs40459	0.84[GIH][hapmap]
rs40544	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs40545	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40547	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs405734	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40635	0.89[CEU][hapmap]
rs40636	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs40638	0.89[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs411310	0.89[CEU][hapmap]
rs416324	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[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];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs419754	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs42343	0.89[CEU][hapmap]
rs42346	0.89[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs42480	0.89[CEU][hapmap]
rs42481	0.84[GIH][hapmap]
rs42490	0.88[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs427854	1.00[YRI][hapmap]
rs428484	0.89[CEU][hapmap]
rs431264	0.82[GIH][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs43134	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs43135	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs43225	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs434264	0.89[CEU][hapmap]
rs447618	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs450332	0.88[CEU][hapmap]
rs454441	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs465	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs51331	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6470366	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6992985	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6993133	0.92[AMR][1000 genomes];0.82[EUR][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	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891181	chr8:90737258-90819998	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs411279	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs411279	RIPK2	Cis_1M	lymphoblastoid	RTeQTL
rs411279	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx
rs411279	RIPK2	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90772200-90809400	Weak transcription	Small Intestine	intestine
2	chr8:90773000-90812400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:90783800-90829000	Weak transcription	Aorta	Aorta
4	chr8:90785600-90813800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr8:90785800-90810800	Weak transcription	Fetal Brain Female	brain
6	chr8:90786000-90813000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:90786400-90809800	Weak transcription	HepG2	liver
8	chr8:90795000-90808400	Weak transcription	NHEK	skin
9	chr8:90797200-90808400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr8:90799400-90810200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr8:90799400-90814000	Weak transcription	Gastric	stomach
12	chr8:90799800-90811800	Weak transcription	Fetal Kidney	kidney
13	chr8:90800000-90808400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr8:90801000-90809600	Weak transcription	Fetal Intestine Small	intestine
15	chr8:90801200-90809800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr8:90802600-90808400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr8:90802600-90808400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:90802600-90808400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:90802600-90809200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr8:90802600-90809600	Weak transcription	Brain Substantia Nigra	brain
21	chr8:90802600-90810200	Weak transcription	Fetal Intestine Large	intestine
22	chr8:90802600-90814200	Weak transcription	K562	blood
23	chr8:90803000-90808400	Weak transcription	HMEC	breast
24	chr8:90803000-90808400	Weak transcription	HUVEC	blood vessel
25	chr8:90803000-90808400	Weak transcription	NHLF	lung
26	chr8:90803000-90811000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr8:90803000-90813400	Weak transcription	Hela-S3	cervix
28	chr8:90803200-90808400	Weak transcription	NH-A	brain
29	chr8:90803200-90810400	Weak transcription	Colonic Mucosa	Colon
30	chr8:90803600-90810400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr8:90803600-90811200	Weak transcription	Primary T cells from cord blood	blood
32	chr8:90803600-90813800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr8:90804200-90808400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr8:90804400-90809200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr8:90804400-90809600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr8:90804600-90808400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:90805200-90808400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr8:90805400-90808200	Weak transcription	Osteobl	bone
39	chr8:90805400-90808400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr8:90805400-90808400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr8:90805400-90817000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr8:90805600-90808400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr8:90805600-90808400	Weak transcription	HSMM	muscle
44	chr8:90805600-90808400	Weak transcription	NHDF-Ad	bronchial
45	chr8:90805600-90809200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr8:90805800-90809600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr8:90806200-90809200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr8:90806200-90814000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr8:90806400-90809600	Weak transcription	Primary B cells from cord blood	blood
50	chr8:90806400-90810200	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links