Variant report

Variant	rs479968
Chromosome Location	chr11:74038274-74038275
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	chr11:74037228..74038762-chr11:74040686..74043088,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1044782	0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1053021	0.93[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10736795	0.91[ASN][1000 genomes]
rs10793072	0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10793073	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs10793074	0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10793075	0.88[ASN][1000 genomes]
rs10793079	0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10793080	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10793081	0.93[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs11236061	0.88[ASN][1000 genomes]
rs11236068	0.84[ASN][1000 genomes]
rs11236087	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11236088	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11559629	0.82[ASN][1000 genomes]
rs2887119	0.93[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs3168173	0.95[ASN][1000 genomes]
rs3741130	0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs3862799	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3867268	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3867270	0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs3867271	0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3867272	0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs480358	0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs486758	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944041	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944887	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs519083	0.88[ASN][1000 genomes]
rs538103	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs563626	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58950228	0.89[ASN][1000 genomes]
rs592644	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs595798	0.88[ASN][1000 genomes]
rs596976	0.93[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs597729	0.84[ASN][1000 genomes]
rs598869	0.93[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs623065	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs625632	0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs634608	0.92[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs637921	0.88[ASN][1000 genomes]
rs641271	0.88[ASN][1000 genomes]
rs646047	0.84[ASN][1000 genomes]
rs655719	0.93[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs657329	0.84[ASN][1000 genomes]
rs662393	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs673103	0.93[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7120394	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7926851	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7928036	0.88[ASN][1000 genomes]
rs7930193	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7934621	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7940145	0.93[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7941916	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7944333	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7945908	0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7947911	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription 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 miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs479968	C2CD3	cis	parietal	SCAN
rs479968	FZD9	trans	brain	seeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74028800-74038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:74031200-74071200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:74033200-74047200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:74033600-74040600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr11:74035000-74038400	Enhancers	Fetal Muscle Leg	muscle
6	chr11:74036200-74038800	Enhancers	Fetal Brain Male	brain
7	chr11:74036400-74038400	Enhancers	Brain Hippocampus Middle	brain
8	chr11:74036400-74038400	Enhancers	Fetal Heart	heart
9	chr11:74036400-74038400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr11:74036600-74038800	Enhancers	HUVEC	blood vessel
11	chr11:74036800-74038400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:74036800-74038400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:74037000-74042800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr11:74037000-74046800	Weak transcription	Fetal Thymus	thymus
15	chr11:74037000-74055400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:74037200-74038400	Enhancers	Adipose Nuclei	Adipose
17	chr11:74037200-74038400	Enhancers	Liver	Liver
18	chr11:74037200-74041000	Weak transcription	Stomach Mucosa	stomach
19	chr11:74037200-74046800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr11:74037200-74050000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr11:74037400-74038600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr11:74037400-74039200	Weak transcription	Thymus	Thymus
23	chr11:74037400-74041000	Weak transcription	NHLF	lung
24	chr11:74037400-74041600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:74037400-74042800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:74037400-74051600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:74037400-74052200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:74037400-74078800	Weak transcription	Small Intestine	intestine
29	chr11:74037600-74040400	Weak transcription	HSMM	muscle
30	chr11:74037600-74041000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:74037600-74041200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:74037600-74041800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:74037600-74042400	Weak transcription	Pancreas	Pancrea
34	chr11:74037600-74051600	Weak transcription	Brain Angular Gyrus	brain
35	chr11:74037600-74052800	Weak transcription	A549	lung
36	chr11:74037800-74040400	Weak transcription	Primary B cells from cord blood	blood
37	chr11:74037800-74040400	Weak transcription	Primary T cells from cord blood	blood
38	chr11:74037800-74040800	Weak transcription	NH-A	brain
39	chr11:74037800-74041200	Weak transcription	NHDF-Ad	bronchial
40	chr11:74037800-74041400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:74037800-74046800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr11:74037800-74086200	Weak transcription	Brain Anterior Caudate	brain
43	chr11:74038000-74040400	Weak transcription	HSMMtube	muscle
44	chr11:74038000-74040600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:74038000-74041200	Weak transcription	Fetal Kidney	kidney
46	chr11:74038000-74041400	Weak transcription	Osteobl	bone
47	chr11:74038000-74044800	Weak transcription	Right Atrium	heart
48	chr11:74038000-74047000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:74038000-74047200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:74038000-74047200	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links