Variant report

Variant	rs6560444
Chromosome Location	chr9:71547032-71547033
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	chr9:71546260..71548319-chr9:71558934..71561181,2	K562	blood:
2	chr9:71545273..71547947-chr9:71556049..71558568,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10114061	0.95[ASN][1000 genomes]
rs10114872	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10115104	0.93[ASN][1000 genomes]
rs10115155	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10115608	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10117043	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10117188	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10122975	0.91[ASN][1000 genomes]
rs10124169	0.95[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10746969	0.87[AMR][1000 genomes]
rs10746979	0.90[CEU][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10781264	0.85[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes]
rs10781265	0.87[AMR][1000 genomes]
rs10781283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781286	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10781293	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10869487	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10869541	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10869543	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10869572	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10869574	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10869578	0.81[ASN][1000 genomes]
rs10869599	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10869607	0.88[ASN][1000 genomes]
rs10869610	0.95[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11143802	0.85[CEU][hapmap]
rs11144476	0.90[CEU][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12337140	0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12349586	0.83[CEU][hapmap]
rs12352694	0.90[AMR][1000 genomes]
rs13300006	0.86[ASN][1000 genomes]
rs2027205	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2152649	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2309384	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4375069	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4745402	0.80[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4745405	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4745451	0.95[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6560420	0.90[CEU][hapmap];0.84[AMR][1000 genomes]
rs6560467	0.81[ASN][1000 genomes]
rs7018692	0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7020192	0.94[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7021212	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7031059	0.95[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs7037010	0.85[ASN][1000 genomes]
rs7041792	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs756326	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7852633	0.85[CEU][hapmap]
rs7853501	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859638	0.82[GIH][hapmap]
rs7867240	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873239	0.90[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv614549	chr9:71506459-71659280	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
19	esv1815996	chr9:71536436-71550717	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv1833433	chr9:71544920-71598165	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6560444	PGM5	cis	cerebellum	SCAN
rs6560444	FAM108B1	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71510400-71576200	Weak transcription	Stomach Mucosa	stomach
2	chr9:71512200-71548800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:71514200-71553600	Weak transcription	Aorta	Aorta
4	chr9:71514200-71557800	Weak transcription	Lung	lung
5	chr9:71519400-71573000	Weak transcription	Gastric	stomach
6	chr9:71532800-71556800	Weak transcription	Right Ventricle	heart
7	chr9:71535000-71569600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:71535200-71547600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr9:71535200-71555400	Weak transcription	Left Ventricle	heart
10	chr9:71535800-71547600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr9:71536200-71548400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:71536600-71557400	Weak transcription	Colonic Mucosa	Colon
13	chr9:71542000-71551600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:71542200-71564400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:71542400-71549800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:71542400-71549800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:71543000-71553600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:71543800-71547200	Strong transcription	Primary B cells from cord blood	blood
19	chr9:71544800-71547800	Strong transcription	Fetal Intestine Large	intestine
20	chr9:71545000-71561600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:71545200-71548000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr9:71545200-71553600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:71545400-71549600	Weak transcription	Fetal Intestine Small	intestine
24	chr9:71545400-71553600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:71545400-71553600	Weak transcription	HepG2	liver
26	chr9:71545400-71562400	Weak transcription	K562	blood
27	chr9:71546000-71547200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr9:71546000-71547200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr9:71546200-71547200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:71546200-71547200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:71546200-71547200	Enhancers	Dnd41	blood
32	chr9:71546200-71547400	Enhancers	Primary T cells from cord blood	blood
33	chr9:71546400-71547200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr9:71546400-71547200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:71546400-71547200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr9:71546400-71547200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr9:71546400-71547400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
38	chr9:71546400-71547400	Enhancers	GM12878-XiMat	blood
39	chr9:71546600-71547200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr9:71546600-71547200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:71546600-71547200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr9:71546600-71547200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:71546600-71547400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr9:71546600-71547400	Enhancers	Pancreas	Pancrea
45	chr9:71546800-71548800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr9:71546800-71561000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr9:71547000-71547200	Enhancers	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links