Variant report

Variant	rs9475861
Chromosome Location	chr6:57211807-57211808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1741910	0.93[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap]
rs1741911	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1741912	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1741913	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1741915	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1755834	0.93[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap]
rs17705499	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs1888265	0.93[ASW][hapmap];0.88[GIH][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap]
rs1888266	0.93[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap]
rs3778513	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs3800007	1.00[JPT][hapmap]
rs3800010	1.00[JPT][hapmap]
rs3800014	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs3800016	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4615395	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs4712146	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs4715652	1.00[JPT][hapmap];0.83[YRI][hapmap]
rs4992408	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs6911353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9296875	1.00[JPT][hapmap]
rs9464434	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9464440	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9475837	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9475844	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs9475845	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9475856	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9475882	1.00[JPT][hapmap]
rs9475887	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2758056	chr6:57184541-57562604	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	esv2759432	chr6:57184541-57562604	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1034139	chr6:57192993-57253423	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1022055	chr6:57192993-57353692	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1015853	chr6:57205882-57528899	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv538231	chr6:57205882-57528899	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1026876	chr6:57205882-57911812	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538232	chr6:57205882-57911812	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1017144	chr6:57205882-58055059	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv538233	chr6:57205882-58055059	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
12	nsv931006	chr6:57205883-58060394	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv603191	chr6:57205920-57381883	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv970125	chr6:57205998-57285497	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
15	esv2453782	chr6:57206998-57575589	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1024888	chr6:57208043-57541463	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1020263	chr6:57208043-57562028	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
18	nsv538234	chr6:57208043-57562028	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1025413	chr6:57208043-57617947	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
20	nsv538235	chr6:57208043-57617947	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
21	nsv1024375	chr6:57208043-58002217	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9475861	COL21A1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57194600-57214800	Weak transcription	Small Intestine	intestine
2	chr6:57194600-57215200	Weak transcription	Ovary	ovary
3	chr6:57194600-57226200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:57194600-57244800	Weak transcription	Spleen	Spleen
5	chr6:57195600-57212600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:57195600-57238400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:57198200-57212400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:57199000-57213800	Weak transcription	K562	blood
9	chr6:57199600-57213200	Weak transcription	HSMM	muscle
10	chr6:57199600-57213400	Weak transcription	Fetal Thymus	thymus
11	chr6:57199600-57214600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:57199600-57214800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:57199600-57215200	Weak transcription	Osteobl	bone
14	chr6:57199600-57221000	Weak transcription	Hela-S3	cervix
15	chr6:57199600-57229000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:57199800-57213200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:57199800-57213400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:57199800-57213800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:57199800-57214600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:57199800-57251000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:57200000-57218000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:57200600-57215000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:57208800-57214000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:57208800-57231200	Weak transcription	Aorta	Aorta
25	chr6:57209000-57244800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:57209200-57213400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:57210200-57213400	Weak transcription	Thymus	Thymus
28	chr6:57210400-57212600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:57210600-57212000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr6:57210600-57212200	ZNF genes & repeats	HepG2	liver
31	chr6:57210600-57212800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:57210800-57212000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:57210800-57212000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr6:57210800-57212400	Genic enhancers	Dnd41	blood
35	chr6:57210800-57212600	Enhancers	H9 Cell Line	embryonic stem cell
36	chr6:57211000-57214000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:57211000-57217800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:57211400-57212000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr6:57211400-57212000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr6:57211400-57212000	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr6:57211400-57212000	ZNF genes & repeats	Primary T cells from cord blood	blood
42	chr6:57211600-57212600	Strong transcription	NHLF	lung
43	chr6:57211800-57212600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:57211800-57214000	Strong transcription	NHDF-Ad	bronchial
45	chr6:57211800-57219000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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