Variant report

Variant	rs11100926
Chromosome Location	chr4:147412403-147412404
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10001383	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10011222	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10012310	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10017463	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10018860	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10024266	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10026558	0.90[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10030464	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10032453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11726588	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11726594	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11727219	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11734649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11940327	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13105153	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13110748	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13134417	0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13134849	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13149918	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13151354	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13435029	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17769016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2357087	0.80[YRI][hapmap]
rs3849037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3914627	0.86[EUR][1000 genomes]
rs3914629	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4835037	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4835040	0.90[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4835307	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4835310	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4835312	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4835313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4835314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4835315	0.90[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4835316	0.90[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6537419	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6537421	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6537423	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6537424	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6537425	1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6537426	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6812728	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6815417	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6816737	0.90[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819042	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6829209	0.90[CEU][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6837453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6840496	0.92[YRI][hapmap]
rs6846498	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6849958	0.84[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7435019	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7437083	0.90[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7439061	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7439429	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7687182	0.85[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7687917	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9992118	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9995307	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9995820	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv917053	chr4:147265436-147499653	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1023868	chr4:147265443-147531626	Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv537293	chr4:147265443-147531626	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv428453	chr4:147335953-147457115	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11100926	TTC29	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147389200-147416200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:147389200-147416400	Weak transcription	NHEK	skin
3	chr4:147399800-147416400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:147402600-147415400	Weak transcription	Gastric	stomach
5	chr4:147403000-147415400	Weak transcription	Ovary	ovary
6	chr4:147403000-147422200	Weak transcription	Placenta	Placenta
7	chr4:147403000-147436200	Weak transcription	Lung	lung
8	chr4:147403800-147424200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:147403800-147440600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:147404200-147441800	Weak transcription	Right Ventricle	heart
11	chr4:147404800-147420400	Weak transcription	Primary B cells from cord blood	blood
12	chr4:147405000-147416200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:147405000-147416200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:147405000-147424400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:147405200-147422600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr4:147405400-147421400	Weak transcription	Liver	Liver
17	chr4:147405400-147422600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:147405400-147424600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:147405400-147436200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:147405400-147440600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:147405600-147417400	Weak transcription	Esophagus	oesophagus
22	chr4:147405600-147417400	Weak transcription	Pancreas	Pancrea
23	chr4:147405600-147421400	Weak transcription	Adipose Nuclei	Adipose
24	chr4:147405600-147440800	Weak transcription	Fetal Intestine Large	intestine
25	chr4:147405800-147422400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:147405800-147422400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:147405800-147428800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:147406400-147435200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr4:147406800-147416200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:147406800-147421800	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:147406800-147424000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:147407000-147422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:147407000-147441800	Weak transcription	Aorta	Aorta
34	chr4:147407200-147441800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:147408200-147416000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:147408200-147417000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr4:147408200-147429600	Weak transcription	Psoas Muscle	Psoas
38	chr4:147408200-147441400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr4:147408200-147442200	Weak transcription	Spleen	Spleen
40	chr4:147408400-147415800	Weak transcription	Small Intestine	intestine
41	chr4:147408600-147416200	Weak transcription	HMEC	breast
42	chr4:147408600-147422600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr4:147408600-147440800	Weak transcription	Fetal Brain Female	brain
44	chr4:147408800-147419600	Weak transcription	Fetal Lung	lung
45	chr4:147409000-147415200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:147409000-147416200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:147409200-147412600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:147409200-147414600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr4:147409200-147418200	Weak transcription	Fetal Intestine Small	intestine
50	chr4:147409200-147422000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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