Variant report

Variant	rs7438704
Chromosome Location	chr4:48363245-48363246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48361503..48363446-chr4:48370042..48372721,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10003230	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10026398	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10029785	0.89[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10938534	0.85[JPT][hapmap]
rs1117010	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11945562	0.85[JPT][hapmap]
rs12503644	0.81[ASN][1000 genomes]
rs12507206	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12511991	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12645501	0.85[JPT][hapmap]
rs12645951	0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12649527	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12649528	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13105385	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13115295	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13133788	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13148849	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13150017	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1352433	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1472967	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1703973	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17656040	0.83[JPT][hapmap]
rs17656094	0.85[JPT][hapmap]
rs2029348	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291474	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291475	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2353312	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28409655	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs368609	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs372825	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828496	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs392187	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs403495	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs404348	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs404445	0.81[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs404656	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs411261	0.89[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs421336	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs421833	0.81[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs429969	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs432927	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs445892	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449376	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs450498	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4536901	0.85[JPT][hapmap]
rs62309425	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447634	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447635	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6811148	0.85[JPT][hapmap]
rs6816010	0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6816352	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6821277	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6829705	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6829716	0.85[JPT][hapmap]
rs6836010	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6836632	0.85[JPT][hapmap]
rs6837335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844211	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6848073	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6848395	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7654770	0.85[JPT][hapmap]
rs7668529	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7672892	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7674269	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7678164	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7678379	0.85[JPT][hapmap]
rs7683398	0.85[JPT][hapmap]
rs7697851	0.85[JPT][hapmap]
rs7700018	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs923372	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs923373	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9291323	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs937888	0.85[JPT][hapmap]
rs952289	0.85[JPT][hapmap]
rs974014	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs974015	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs974016	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs992423	0.85[JPT][hapmap]
rs9996532	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7438704	SLAIN2	cis	parietal	SCAN
rs7438704	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL
rs7438704	OCIAD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:48349600-48364400	Weak transcription	Right Atrium	heart
5	chr4:48350000-48375800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr4:48352800-48372400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:48353000-48371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:48353800-48369200	Weak transcription	Pancreas	Pancrea
9	chr4:48355000-48376600	Weak transcription	Primary B cells from cord blood	blood
10	chr4:48355000-48380000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
12	chr4:48355200-48377600	Weak transcription	Fetal Intestine Small	intestine
13	chr4:48355200-48379800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:48355400-48371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:48356600-48367800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:48357200-48384600	Weak transcription	Lung	lung
18	chr4:48358400-48367000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:48358800-48371800	Weak transcription	Small Intestine	intestine
20	chr4:48359200-48384400	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:48361000-48384600	Weak transcription	Fetal Stomach	stomach
22	chr4:48361600-48363600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:48361800-48364000	Enhancers	HMEC	breast
24	chr4:48362000-48363400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:48362200-48363400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr4:48362200-48363400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr4:48362200-48363600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:48362200-48363600	Enhancers	Brain Cingulate Gyrus	brain
29	chr4:48362200-48363600	Enhancers	Colon Smooth Muscle	Colon
30	chr4:48362200-48363600	Enhancers	NHLF	lung
31	chr4:48362200-48363800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr4:48362200-48363800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:48362200-48363800	Enhancers	Fetal Brain Female	brain
34	chr4:48362200-48364000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr4:48362200-48364000	Enhancers	Brain Angular Gyrus	brain
36	chr4:48362200-48364000	Enhancers	Fetal Heart	heart
37	chr4:48362200-48364000	Enhancers	NHDF-Ad	bronchial
38	chr4:48362200-48364400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr4:48362400-48363400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:48362400-48363400	Enhancers	Stomach Smooth Muscle	stomach
41	chr4:48362400-48363600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr4:48362400-48363600	Enhancers	HSMM	muscle
43	chr4:48362400-48364600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:48362600-48363400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:48362600-48363800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:48362600-48364200	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr4:48362600-48378000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:48362600-48378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:48362600-48384600	Weak transcription	Left Ventricle	heart
50	chr4:48362800-48363400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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