Variant report

Variant	rs9470723
Chromosome Location	chr6:37835649-37835650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37785357..37787655-chr6:37832956..37835943,2	K562	blood:
2	chr6:37835497..37837699-chr6:37850167..37852091,2	MCF-7	breast:
3	chr6:37827459..37830301-chr6:37832209..37835878,4	MCF-7	breast:
4	chr6:37835143..37837500-chr6:37850696..37852776,2	MCF-7	breast:
5	chr6:37834905..37837847-chr6:37840827..37844123,3	MCF-7	breast:
6	chr6:37831139..37833570-chr6:37835178..37837982,3	K562	blood:

Variant related genes	Relation type
ENSG00000225945	Chromatin interaction
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11756656	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1212636	0.85[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12211975	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs174105	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs187741	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1979759	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2055205	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2180514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2201646	0.92[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2395687	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs259672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs259674	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs259675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259676	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs259677	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs259678	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs259682	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs259685	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259687	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259688	0.85[ASN][1000 genomes]
rs259693	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259694	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259714	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259717	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs259721	0.85[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs259722	0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs259723	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3792706	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4142102	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4711522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711524	0.81[ASN][1000 genomes]
rs4714118	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4714123	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs6458030	0.92[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458036	0.84[ASN][1000 genomes]
rs67133782	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67479083	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6912097	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6915506	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6917668	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6920185	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6926280	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs6930859	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs6934617	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765798	0.92[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs9357255	0.83[MEX][hapmap]
rs9369029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs9394469	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9462374	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs9470714	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9470724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470725	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9647620	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1016375	chr6:37816863-37865655	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv538204	chr6:37816863-37865655	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9470723	LRFN2	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37800200-37836200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:37808000-37839000	Weak transcription	Fetal Stomach	stomach
3	chr6:37812600-37836000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:37813600-37845200	Weak transcription	K562	blood
5	chr6:37818400-37836000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:37820000-37850200	Weak transcription	Fetal Kidney	kidney
7	chr6:37820400-37836000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:37824000-37842000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:37824400-37836200	Weak transcription	Fetal Intestine Large	intestine
10	chr6:37826800-37836200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:37829000-37837800	Weak transcription	Dnd41	blood
12	chr6:37831000-37836000	Weak transcription	Hela-S3	cervix
13	chr6:37831000-37836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:37831000-37846000	Weak transcription	Esophagus	oesophagus
15	chr6:37831200-37837000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr6:37831200-37839600	Weak transcription	Fetal Lung	lung
17	chr6:37831400-37836000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:37831600-37836600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:37831800-37836400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:37832000-37836000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:37832400-37836200	Weak transcription	Fetal Brain Male	brain
22	chr6:37832600-37836400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr6:37832800-37836000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:37832800-37836200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:37833000-37835800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:37833000-37836200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:37833000-37836200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:37833000-37836400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:37833000-37837000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr6:37833000-37837600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr6:37833200-37836000	Enhancers	Osteobl	bone
32	chr6:37833200-37836200	Enhancers	Primary T cells from cord blood	blood
33	chr6:37833200-37836800	Enhancers	HSMM	muscle
34	chr6:37833400-37835800	Enhancers	Brain Hippocampus Middle	brain
35	chr6:37833400-37836400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr6:37833400-37836400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:37833400-37836600	Enhancers	Primary B cells from peripheral blood	blood
38	chr6:37833400-37836600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr6:37833600-37836200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:37833600-37836400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:37833600-37836600	Enhancers	Rectal Smooth Muscle	rectum
42	chr6:37833600-37836600	Enhancers	A549	lung
43	chr6:37833800-37837000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:37834000-37836000	Weak transcription	Aorta	Aorta
45	chr6:37834000-37836200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr6:37834000-37836400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr6:37834000-37837800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:37834000-37838000	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:37834000-37845800	Weak transcription	Spleen	Spleen
50	chr6:37834000-37846000	Weak transcription	Lung	lung

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