Variant report

Variant	rs4373935
Chromosome Location	chr11:120273301-120273302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10502236	1.00[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs10892573	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10892579	1.00[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs10892580	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10892581	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217837	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11217847	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217853	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11217859	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217860	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217861	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11217865	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217868	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217869	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217871	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217872	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11217873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217879	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217881	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217883	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217889	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600200	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600558	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600723	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602796	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606928	1.00[ASN][1000 genomes]
rs11607944	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820277	1.00[ASN][1000 genomes]
rs12361340	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12361642	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362794	1.00[CEU][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs12363974	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12363975	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120430	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35912781	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537767	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56329702	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57912596	0.94[EUR][1000 genomes]
rs61072783	1.00[ASN][1000 genomes]
rs61898267	1.00[ASN][1000 genomes]
rs61898282	1.00[ASN][1000 genomes]
rs61898283	1.00[ASN][1000 genomes]
rs61898284	1.00[ASN][1000 genomes]
rs61898287	1.00[ASN][1000 genomes]
rs61898768	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61900794	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61900795	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67551874	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67617613	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7108596	0.94[EUR][1000 genomes]
rs7110955	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs7120040	0.85[EUR][1000 genomes]
rs7120174	1.00[CEU][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs73582205	1.00[ASN][1000 genomes]
rs73584117	1.00[ASN][1000 genomes]
rs73584140	1.00[ASN][1000 genomes]
rs73584846	1.00[ASN][1000 genomes]
rs73584849	1.00[ASN][1000 genomes]
rs73584865	1.00[ASN][1000 genomes]
rs747419	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs766894	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943147	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7948299	0.91[EUR][1000 genomes]
rs9625	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9666435	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9666441	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv529003	chr11:120209386-120355230	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1050935	chr11:120224544-120276373	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1036694	chr11:120230243-120285603	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1037573	chr11:120230243-120286918	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1047982	chr11:120238962-120276373	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1050789	chr11:120238962-120286918	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1046430	chr11:120238962-120294026	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1043248	chr11:120238962-120299598	Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1051672	chr11:120238962-120314178	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1050709	chr11:120246224-120276373	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1051783	chr11:120246224-120314178	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4373935	ZNF259	cis	cerebellum	SCAN
rs4373935	UPK2	cis	cerebellum	SCAN
rs4373935	MPZL3	cis	parietal	SCAN
rs4373935	TMEM136	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120232000-120274800	Weak transcription	Ovary	ovary
2	chr11:120263600-120274600	Weak transcription	Right Ventricle	heart
3	chr11:120265800-120295600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:120266600-120274000	Weak transcription	Left Ventricle	heart
5	chr11:120266800-120274000	Weak transcription	Gastric	stomach
6	chr11:120267800-120274600	Weak transcription	Fetal Heart	heart
7	chr11:120269200-120295200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:120269400-120274400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:120269400-120283000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:120270000-120273400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr11:120270000-120273800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr11:120270400-120292200	Weak transcription	Fetal Stomach	stomach
13	chr11:120271600-120300200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:120271800-120274400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:120271800-120274400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:120272000-120274400	Weak transcription	K562	blood
17	chr11:120272000-120274800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:120272000-120274800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:120272000-120279600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr11:120272000-120283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:120272000-120287000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:120272000-120287000	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:120272000-120288400	Weak transcription	Aorta	Aorta
24	chr11:120272000-120291200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr11:120272000-120291400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr11:120272000-120302400	Weak transcription	Brain Anterior Caudate	brain
27	chr11:120272200-120274400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:120272200-120274400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:120272200-120274400	Weak transcription	Stomach Mucosa	stomach
30	chr11:120272200-120274800	Enhancers	A549	lung
31	chr11:120272200-120279600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:120272200-120283000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:120272200-120291400	Weak transcription	GM12878-XiMat	blood
34	chr11:120272200-120292600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:120272200-120292800	Weak transcription	Fetal Kidney	kidney
36	chr11:120272200-120295200	Weak transcription	Brain Angular Gyrus	brain
37	chr11:120272200-120295200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:120272200-120299000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr11:120272200-120315600	Weak transcription	Brain Germinal Matrix	brain
40	chr11:120272200-120315800	Weak transcription	Brain Hippocampus Middle	brain
41	chr11:120272400-120273400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:120272400-120273400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr11:120272400-120273400	Enhancers	HSMM	muscle
44	chr11:120272400-120273400	Enhancers	NHEK	skin
45	chr11:120272400-120273600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr11:120272400-120274000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:120272400-120274000	Weak transcription	Small Intestine	intestine
48	chr11:120272400-120274400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:120272400-120274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:120272400-120274800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links