Variant report

Variant	rs979942
Chromosome Location	chr11:4185595-4185596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:4115681..4117881-chr11:4185154..4187618,2	K562	blood:
2	chr11:4184965..4187541-chr11:4189558..4191938,3	K562	blood:
3	chr11:4184965..4186583-chr11:4189758..4191938,2	K562	blood:

Variant related genes	Relation type
ENSG00000167325	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10128744	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734406	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742251	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767872	0.86[ASN][1000 genomes]
rs10767878	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10767881	0.84[ASN][1000 genomes]
rs10767882	0.84[ASN][1000 genomes]
rs10767886	0.84[ASN][1000 genomes]
rs10767891	0.81[CHB][hapmap]
rs10835694	0.86[ASN][1000 genomes]
rs10835695	0.86[ASN][1000 genomes]
rs10835699	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835701	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835719	0.81[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10835722	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10835723	0.84[ASN][1000 genomes]
rs10835729	0.84[ASN][1000 genomes]
rs10835734	0.84[ASN][1000 genomes]
rs10835735	0.84[ASN][1000 genomes]
rs10835736	0.84[ASN][1000 genomes]
rs10835743	0.83[ASN][1000 genomes]
rs11031156	0.86[ASN][1000 genomes]
rs11031157	0.84[ASN][1000 genomes]
rs11031182	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11031184	0.87[CHB][hapmap];0.87[JPT][hapmap];0.98[ASN][1000 genomes]
rs11031214	0.83[ASN][1000 genomes]
rs11031219	0.84[ASN][1000 genomes]
rs11031220	0.84[ASN][1000 genomes]
rs11031243	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11031244	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11031245	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11031252	0.84[ASN][1000 genomes]
rs12221831	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12222136	0.86[ASN][1000 genomes]
rs12222147	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12223062	0.86[ASN][1000 genomes]
rs12225982	0.86[ASN][1000 genomes]
rs12270809	0.84[ASN][1000 genomes]
rs12275560	0.84[ASN][1000 genomes]
rs12275634	0.84[ASN][1000 genomes]
rs12281849	0.83[ASN][1000 genomes]
rs12289940	0.83[ASN][1000 genomes]
rs12292515	0.84[ASN][1000 genomes]
rs12292724	0.86[ASN][1000 genomes]
rs12293706	0.84[ASN][1000 genomes]
rs12295191	0.84[ASN][1000 genomes]
rs1348308	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1348309	0.84[ASN][1000 genomes]
rs1348312	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1372806	0.84[ASN][1000 genomes]
rs1442727	0.86[ASN][1000 genomes]
rs1442728	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17283923	0.86[ASN][1000 genomes]
rs17284356	0.84[ASN][1000 genomes]
rs1822288	0.84[ASN][1000 genomes]
rs1822289	0.84[ASN][1000 genomes]
rs2044135	0.87[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs34295904	0.84[ASN][1000 genomes]
rs34600103	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34805399	0.84[ASN][1000 genomes]
rs35898891	0.84[ASN][1000 genomes]
rs4399325	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4606468	0.86[ASN][1000 genomes]
rs4631873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899754	0.84[ASN][1000 genomes]
rs61899755	0.84[ASN][1000 genomes]
rs7103651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130265	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7131300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7479886	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930812	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933127	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933808	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948575	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935130	0.80[ASN][1000 genomes]
rs970329	0.84[ASN][1000 genomes]
rs970330	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs979941	0.93[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1053189	chr11:4123119-4359044	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1048590	chr11:4133055-4225100	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv540911	chr11:4133055-4225100	Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1053482	chr11:4138062-4276133	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3380413	chr11:4159374-4323846	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv8777	chr11:4159953-4387268	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1045527	chr11:4162019-4225100	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv34983	chr11:4162474-4325792	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	esv2757417	chr11:4162477-4325792	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv818795	chr11:4167416-4238930	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv467662	chr11:4185595-4272343	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv553151	chr11:4185595-4272343	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs979942	TRIM3	cis	cerebellum	SCAN
rs979942	OR52W1	cis	parietal	SCAN
rs979942	OR51E2	cis	cerebellum	SCAN
rs979942	ART5	cis	cerebellum	SCAN
rs979942	LRRC56	cis	parietal	SCAN
rs979942	RIC3	cis	parietal	SCAN
rs979942	PTGS1	trans	lymphoblastoid	seeQTL
rs979942	INS-IGF2	cis	cerebellum	SCAN
rs979942	IGF2AS	cis	cerebellum	SCAN
rs979942	OR52I2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4178800-4187800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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