Variant report

Variant	rs12641947
Chromosome Location	chr4:2869815-2869816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2868702..2870783-chr4:2881589..2883580,3	K562	blood:
2	chr4:2867681..2870567-chr4:2936383..2939288,2	MCF-7	breast:
3	chr2:226959307..226961604-chr4:2869808..2871481,2	MCF-7	breast:
4	chr4:2866956..2870306-chr4:2932983..2937533,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BP2-2	chr4:2869699-2869822	NONHSAT094815

Variant related genes	Relation type
ENSG00000249673	Chromatin interaction
ENSG00000109736	Chromatin interaction
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10026792	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1263412	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17833172	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17833250	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1877723	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2032470	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2096760	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35780153	0.88[ASN][1000 genomes]
rs55927173	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58115360	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59150074	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs624833	0.92[ASN][1000 genomes]
rs6600769	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6819310	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824567	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7655104	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678161	0.84[ASN][1000 genomes]

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	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	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12641947	GRK4	cis	Artery Tibial	GTEx
rs12641947	GRK4	cis	Thyroid	GTEx
rs12641947	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs12641947	GRK4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2857000-2877000	Weak transcription	Dnd41	blood
2	chr4:2857400-2870000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr4:2857400-2877600	Weak transcription	HMEC	breast
4	chr4:2860800-2871000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:2861400-2872600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:2864600-2877400	Weak transcription	NHEK	skin
7	chr4:2864800-2873200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:2865600-2870200	Weak transcription	Placenta	Placenta
9	chr4:2865600-2871200	Enhancers	Primary hematopoietic stem cells	blood
10	chr4:2865600-2871400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:2866200-2872400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:2866600-2870200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:2866800-2872200	Enhancers	Fetal Heart	heart
14	chr4:2867400-2871400	Weak transcription	A549	lung
15	chr4:2867400-2873200	Weak transcription	GM12878-XiMat	blood
16	chr4:2867800-2871000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr4:2868000-2871600	Enhancers	Brain Germinal Matrix	brain
18	chr4:2868200-2871600	Enhancers	Small Intestine	intestine
19	chr4:2868400-2870200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr4:2868400-2871400	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr4:2868400-2872600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:2868400-2872600	Enhancers	Fetal Intestine Large	intestine
23	chr4:2868600-2870000	Enhancers	Fetal Thymus	thymus
24	chr4:2868600-2870400	Genic enhancers	Primary T cells from cord blood	blood
25	chr4:2868600-2870400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr4:2868600-2871200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr4:2868600-2871200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:2868600-2871400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr4:2868800-2870200	Enhancers	Primary B cells from cord blood	blood
30	chr4:2868800-2870200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:2868800-2870800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr4:2868800-2870800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:2868800-2872000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr4:2869000-2870200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:2869000-2870600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:2869000-2870600	Weak transcription	Spleen	Spleen
37	chr4:2869000-2871000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr4:2869000-2871200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr4:2869000-2872200	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr4:2869200-2870200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr4:2869200-2870200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr4:2869200-2870200	Flanking Active TSS	K562	blood
43	chr4:2869200-2870600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr4:2869200-2870600	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr4:2869200-2870600	Flanking Active TSS	NHDF-Ad	bronchial
46	chr4:2869200-2870800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:2869200-2871000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:2869200-2871200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:2869200-2872600	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr4:2869400-2870000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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