Variant report

Variant	rs4979170
Chromosome Location	chr9:115626918-115626919
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115623112..115625247-chr9:115625662..115630540,4	K562	blood:
2	chr9:115622331..115624612-chr9:115626867..115628416,2	K562	blood:
3	chr9:115615876..115617436-chr9:115625877..115628749,2	MCF-7	breast:
4	chr9:115625288..115627848-chr9:115629822..115631773,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10114602	0.92[EUR][1000 genomes]
rs10114623	0.92[EUR][1000 genomes]
rs10115576	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs10115711	0.82[CEU][hapmap]
rs10116897	0.92[EUR][1000 genomes]
rs10124260	0.85[CEU][hapmap]
rs10124939	0.82[CEU][hapmap]
rs10124979	0.82[CEU][hapmap]
rs1041086	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10733594	0.85[CEU][hapmap]
rs10733598	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10733599	1.00[CEU][hapmap]
rs10739370	0.82[CEU][hapmap]
rs10739373	0.85[CEU][hapmap]
rs10739376	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10739377	0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs10739378	1.00[CEU][hapmap];0.94[YRI][hapmap];0.94[EUR][1000 genomes]
rs10739379	0.94[EUR][1000 genomes]
rs10759590	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10759603	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs10759604	0.94[EUR][1000 genomes]
rs10981534	0.92[EUR][1000 genomes]
rs11794827	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12684608	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12685729	0.90[ASN][1000 genomes]
rs12686253	0.82[ASN][1000 genomes]
rs1324930	0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs1324931	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs1324932	0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs1361720	0.85[CEU][hapmap]
rs1418409	0.85[CEU][hapmap]
rs1475293	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1539338	0.85[CEU][hapmap]
rs16917411	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1891402	0.85[CEU][hapmap]
rs1891403	0.85[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs2025544	1.00[CEU][hapmap]
rs2645993	0.85[CEU][hapmap]
rs2796028	0.85[CEU][hapmap]
rs4246892	0.85[CEU][hapmap]
rs4304397	0.85[CEU][hapmap]
rs4978507	0.85[CEU][hapmap]
rs4978509	0.92[EUR][1000 genomes]
rs4978511	0.82[CEU][hapmap]
rs4979153	0.85[CEU][hapmap]
rs4979154	0.85[CEU][hapmap]
rs4979157	0.85[CEU][hapmap]
rs4979165	0.85[CEU][hapmap]
rs4979173	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4979175	0.92[EUR][1000 genomes]
rs4979176	0.94[EUR][1000 genomes]
rs4979177	0.86[EUR][1000 genomes]
rs4979178	0.86[EUR][1000 genomes]
rs62576453	0.91[EUR][1000 genomes]
rs6477959	0.85[CEU][hapmap]
rs700122	0.85[CEU][hapmap]
rs7023956	0.82[EUR][1000 genomes]
rs7030795	0.85[CEU][hapmap]
rs7047914	0.87[EUR][1000 genomes]
rs7859175	0.85[CEU][hapmap]
rs7868830	0.85[CEU][hapmap]
rs787271	0.85[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs787274	0.83[GIH][hapmap]
rs787276	0.85[CEU][hapmap]
rs787280	0.85[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs787284	0.85[CEU][hapmap]
rs787287	0.85[CEU][hapmap]
rs787294	0.85[CEU][hapmap]
rs787295	0.85[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs787297	0.85[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs787298	0.85[CEU][hapmap]
rs787299	0.85[CEU][hapmap]
rs787301	0.85[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs787302	0.85[CEU][hapmap]
rs7873289	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs813101	0.85[CEU][hapmap]
rs885387	0.85[CEU][hapmap]
rs9409123	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv2757351	chr9:115600623-115632898	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4979170	TSCOT	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:115594200-115634400	Weak transcription	NH-A	brain
4	chr9:115601200-115641200	Weak transcription	Fetal Brain Male	brain
5	chr9:115607400-115643400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:115607600-115630200	Weak transcription	NHEK	skin
7	chr9:115611400-115628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:115611400-115634600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:115611600-115630200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:115611600-115634200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:115611800-115630200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:115612000-115634600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:115613600-115628200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr9:115613600-115642600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr9:115614000-115632600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:115614200-115630200	Weak transcription	Fetal Brain Female	brain
17	chr9:115615200-115630200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:115615600-115630000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr9:115615600-115630200	Weak transcription	HMEC	breast
20	chr9:115615600-115631000	Weak transcription	Psoas Muscle	Psoas
21	chr9:115615600-115639200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:115615600-115646400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:115615800-115628600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:115616000-115630000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:115616000-115631400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr9:115616800-115627000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr9:115617000-115628600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:115617000-115628800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:115617000-115630200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:115617200-115627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:115617600-115629800	Weak transcription	HSMMtube	muscle
32	chr9:115618000-115630200	Weak transcription	HSMM	muscle
33	chr9:115620600-115631000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr9:115621200-115639400	Weak transcription	Stomach Mucosa	stomach
35	chr9:115621600-115629800	Strong transcription	Fetal Intestine Small	intestine
36	chr9:115622400-115627000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:115622400-115627400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr9:115622800-115627600	Enhancers	Primary B cells from peripheral blood	blood
39	chr9:115623000-115627200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:115623000-115627600	Enhancers	Primary hematopoietic stem cells	blood
41	chr9:115623200-115627800	Enhancers	Fetal Thymus	thymus
42	chr9:115623600-115627200	Weak transcription	HepG2	liver
43	chr9:115623600-115630200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:115624200-115629200	Enhancers	Adipose Nuclei	Adipose
45	chr9:115624200-115652600	Weak transcription	Fetal Heart	heart
46	chr9:115624400-115630200	Weak transcription	Right Ventricle	heart
47	chr9:115624600-115628200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:115624600-115628600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr9:115624800-115627200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr9:115624800-115627200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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