Variant report

Variant	rs2471325
Chromosome Location	chr4:3024044-3024045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:3023920-3024070	GM12865	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3022979..3027638-chr4:3028157..3033306,5	K562	blood:

Variant related genes	Relation type
GRK4	TF binding region
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10021191	0.89[ASN][1000 genomes]
rs10030130	0.89[ASN][1000 genomes]
rs1056094	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs11937729	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12643541	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1419046	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16843629	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs16843684	0.89[ASN][1000 genomes]
rs1891710	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2022485	1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2040061	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2051555	1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2051556	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2051557	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2153997	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2185887	0.89[ASN][1000 genomes]
rs2185888	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2251457	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2298966	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2471322	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471323	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471324	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471335	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471336	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471337	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471338	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471339	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471340	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471346	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471351	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2488813	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs2488816	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2488817	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2488818	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2515935	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2515936	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2515938	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2515939	0.89[ASN][1000 genomes]
rs2515940	0.89[ASN][1000 genomes]
rs2515941	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2515942	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2515943	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs2515963	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.80[EUR][1000 genomes]
rs28414352	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28619042	0.81[ASN][1000 genomes]
rs28666534	0.89[ASN][1000 genomes]
rs2960298	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960303	0.87[ASN][1000 genomes]
rs2960306	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960307	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960310	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2995803	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2995804	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3021136	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3021138	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3021139	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3021140	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3021141	0.89[ASN][1000 genomes]
rs3021142	0.89[ASN][1000 genomes]
rs3021146	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs56214407	0.82[ASN][1000 genomes]
rs6446720	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7667520	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7678019	0.89[ASN][1000 genomes]
rs7690813	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7696434	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv1008436	chr4:2947160-3031195	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv536998	chr4:2947160-3031195	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv593438	chr4:2948456-3030097	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2471325	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs2471325	GRK4	cis	parietal	SCAN
rs2471325	GRK4	cis	Adipose Subcutaneous	GTEx
rs2471325	GRK4	cis	lung	GTEx
rs2471325	GRK4	cis	Thyroid	GTEx
rs2471325	GRK4	cis	cerebellum	SCAN
rs2471325	GRK4	cis	Artery Tibial	GTEx
rs2471325	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs2471325	NOP14	cis	cerebellum	SCAN
rs2471325	GRK4	cis	Artery Aorta	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2979600-3025000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:2983600-3032000	Weak transcription	Fetal Brain Female	brain
3	chr4:2991400-3024600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:3003800-3024600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:3005800-3038600	Weak transcription	Right Ventricle	heart
6	chr4:3007600-3024600	Weak transcription	Brain Angular Gyrus	brain
7	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
8	chr4:3012800-3024800	Weak transcription	Aorta	Aorta
9	chr4:3014600-3026200	Weak transcription	Fetal Brain Male	brain
10	chr4:3014800-3025000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:3016200-3033200	Weak transcription	Pancreas	Pancrea
12	chr4:3019200-3039000	Weak transcription	Left Ventricle	heart
13	chr4:3019800-3024600	Weak transcription	HSMMtube	muscle
14	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
15	chr4:3021600-3024600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:3021800-3024600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:3023200-3024800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:3023600-3024800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr4:3023800-3024400	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links