Variant report

Variant	rs13103523
Chromosome Location	chr4:78682742-78682743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10033527	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10033613	0.85[ASN][1000 genomes]
rs11097938	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11728886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11729215	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12645742	0.95[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13101418	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs13101987	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13103035	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13104947	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13106067	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs13119606	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13120272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16996915	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2134050	0.85[ASN][1000 genomes]
rs34830788	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35735677	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4453957	0.85[ASN][1000 genomes]
rs4577601	1.00[JPT][hapmap]
rs4859509	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4859511	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4859875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859877	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859879	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859889	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6533282	0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs6533291	0.85[ASN][1000 genomes]
rs6533344	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6814912	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs6848029	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6854895	1.00[JPT][hapmap]
rs7670157	0.89[JPT][hapmap]
rs7675009	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7698627	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv518757	chr4:78637265-78695138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13103523	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
2	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
3	chr4:78643800-78714000	Weak transcription	Lung	lung
4	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
6	chr4:78650200-78697800	Weak transcription	Gastric	stomach
7	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
10	chr4:78650800-78697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:78654200-78697600	Weak transcription	HSMMtube	muscle
12	chr4:78657000-78695600	Weak transcription	Small Intestine	intestine
13	chr4:78659800-78685800	Weak transcription	Psoas Muscle	Psoas
14	chr4:78659800-78697800	Weak transcription	Esophagus	oesophagus
15	chr4:78662000-78695600	Weak transcription	Ovary	ovary
16	chr4:78662000-78697600	Weak transcription	Brain Angular Gyrus	brain
17	chr4:78662000-78697800	Weak transcription	Pancreas	Pancrea
18	chr4:78662200-78697800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:78662800-78683400	Weak transcription	Fetal Kidney	kidney
20	chr4:78662800-78683600	Weak transcription	K562	blood
21	chr4:78663800-78695600	Weak transcription	Left Ventricle	heart
22	chr4:78673400-78687000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:78673400-78692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:78676200-78683400	Weak transcription	GM12878-XiMat	blood
25	chr4:78676200-78687400	Strong transcription	Fetal Thymus	thymus
26	chr4:78677400-78682800	Strong transcription	Dnd41	blood
27	chr4:78677800-78693800	Weak transcription	Hela-S3	cervix
28	chr4:78677800-78698400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:78678000-78691200	Weak transcription	Placenta	Placenta
30	chr4:78678000-78691800	Weak transcription	HUVEC	blood vessel
31	chr4:78678000-78692400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:78678000-78698400	Weak transcription	HSMM	muscle
33	chr4:78678400-78692600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:78679200-78683600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:78679400-78684000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:78679600-78686600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:78680200-78683800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:78681200-78682800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr4:78681200-78692800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr4:78681600-78684000	ZNF genes & repeats	Fetal Brain Female	brain
41	chr4:78681600-78692200	Weak transcription	Fetal Stomach	stomach
42	chr4:78681800-78683600	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr4:78682000-78684200	ZNF genes & repeats	Primary T cells from cord blood	blood
44	chr4:78682000-78685600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:78682200-78682800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
46	chr4:78682200-78682800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:78682200-78684000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:78682200-78684000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr4:78682200-78684000	ZNF genes & repeats	Liver	Liver
50	chr4:78682200-78684000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links