Variant report

Variant	rs7649234
Chromosome Location	chr3:47494380-47494381
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47490125..47492275-chr3:47492500..47495080,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1038394	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865946	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130128	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130129	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130132	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130133	0.88[EUR][1000 genomes]
rs11130137	0.84[EUR][1000 genomes]
rs11705957	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11707895	0.85[EUR][1000 genomes]
rs11711265	0.88[EUR][1000 genomes]
rs11711824	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712445	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11713413	0.83[EUR][1000 genomes]
rs11716763	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11719877	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11914913	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11914932	0.88[EUR][1000 genomes]
rs11925823	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12486969	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12487736	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12489046	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490058	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490383	0.83[ASN][1000 genomes]
rs12492433	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12497225	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12630641	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12632132	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12636851	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13059519	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13064843	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13075233	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13079098	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1531875	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17080872	0.81[ASN][1000 genomes]
rs17784882	0.90[EUR][1000 genomes]
rs1872164	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2062278	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2101247	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291298	0.88[EUR][1000 genomes]
rs34634681	0.84[EUR][1000 genomes]
rs3736177	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3816779	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4241548	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4599332	0.84[EUR][1000 genomes]
rs4858805	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858848	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858856	0.86[EUR][1000 genomes]
rs4858868	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858894	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs553989	0.83[AMR][1000 genomes]
rs56032309	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56351005	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57346147	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59586735	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60369822	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62248599	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62248603	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62248605	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62260710	0.87[EUR][1000 genomes]
rs62260711	0.87[EUR][1000 genomes]
rs62260741	0.82[EUR][1000 genomes]
rs6765990	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6780013	0.80[EUR][1000 genomes]
rs6787422	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6790763	0.83[EUR][1000 genomes]
rs6792461	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792488	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6800271	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73081205	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7628631	0.88[EUR][1000 genomes]
rs7641010	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7651194	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651762	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs807810	0.80[EUR][1000 genomes]
rs878659	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs922957	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9683033	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9683177	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv590212	chr3:47485029-47500662	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3461079	chr3:47488748-47495346	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv3806	chr3:47488784-47518133	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv3489698	chr3:47489548-47494546	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3489693	chr3:47489973-47494471	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1816532	chr3:47490712-47511698	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv1841538	chr3:47490712-47511698	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv1848062	chr3:47490712-47511698	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv1849930	chr3:47490712-47511698	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7649234	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs7649234	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47476600-47514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:47481400-47496000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:47481400-47500600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47484000-47507800	Weak transcription	Primary B cells from cord blood	blood
5	chr3:47484000-47511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:47484200-47511200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:47484400-47497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:47484600-47497400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:47484600-47500600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:47484600-47514000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:47484600-47514200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:47484600-47514200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:47484600-47514200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:47484600-47514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:47484800-47504400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:47484800-47504600	Weak transcription	Primary T cells from cord blood	blood
17	chr3:47484800-47514800	Weak transcription	Thymus	Thymus
18	chr3:47485000-47514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:47485200-47502600	Weak transcription	K562	blood
20	chr3:47485400-47503200	Weak transcription	Gastric	stomach
21	chr3:47486000-47497200	Weak transcription	A549	lung
22	chr3:47486000-47497400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:47486000-47500200	Weak transcription	Fetal Intestine Large	intestine
24	chr3:47486000-47500400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:47486000-47504600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:47486000-47516000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:47486000-47516000	Weak transcription	Small Intestine	intestine
28	chr3:47486000-47516000	Weak transcription	HSMM	muscle
29	chr3:47486200-47497200	Weak transcription	Hela-S3	cervix
30	chr3:47486200-47502600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:47486200-47506000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:47486200-47516000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:47486600-47494400	Weak transcription	HepG2	liver
34	chr3:47486600-47500600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:47487000-47502400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:47487400-47497600	Weak transcription	Liver	Liver
37	chr3:47489200-47500400	Weak transcription	Fetal Intestine Small	intestine
38	chr3:47491000-47494400	Weak transcription	Pancreas	Pancrea
39	chr3:47492200-47494800	Enhancers	Psoas Muscle	Psoas
40	chr3:47493400-47496400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:47493400-47510800	Weak transcription	Spleen	Spleen
42	chr3:47494000-47494400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr3:47494000-47494400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr3:47494000-47494600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:47494000-47497200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:47494000-47503000	Weak transcription	Right Ventricle	heart
47	chr3:47494200-47494400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:47494200-47494400	Enhancers	Stomach Mucosa	stomach
49	chr3:47494200-47494600	Enhancers	Esophagus	oesophagus
50	chr3:47494200-47494600	ZNF genes & repeats	Fetal Stomach	stomach

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