Variant report

Variant	rs55687343
Chromosome Location	chr1:174251675-174251676
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs55669124	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55773127	0.87[AFR][1000 genomes]
rs55833532	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56058592	0.82[AMR][1000 genomes]
rs56106938	0.81[AFR][1000 genomes]
rs56179605	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56185645	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56204297	0.87[AFR][1000 genomes]
rs56223691	0.87[AFR][1000 genomes]
rs56234951	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56713956	0.81[AFR][1000 genomes]
rs57774157	0.81[AFR][1000 genomes]
rs58066823	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58831567	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58842085	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58997380	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59102371	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59753012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60717080	0.81[AFR][1000 genomes]
rs61077309	0.87[AFR][1000 genomes]
rs61288130	0.87[AFR][1000 genomes]
rs74126804	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126807	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126808	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126812	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126813	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126815	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126817	1.00[ASN][1000 genomes]
rs74126818	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126819	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126820	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128317	0.81[AFR][1000 genomes]
rs74128318	0.81[AFR][1000 genomes]
rs74128319	0.81[AFR][1000 genomes]
rs74128320	0.87[AFR][1000 genomes]
rs74128321	0.87[AFR][1000 genomes]
rs74128322	0.81[AFR][1000 genomes]
rs74128323	0.81[AFR][1000 genomes]
rs74128324	0.81[AFR][1000 genomes]
rs74128326	0.81[AFR][1000 genomes]
rs74128329	0.81[AFR][1000 genomes]
rs74128334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128335	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128338	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128342	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128343	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128344	0.87[AFR][1000 genomes]
rs74128345	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128346	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128348	1.00[ASN][1000 genomes]
rs74128349	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128350	1.00[ASN][1000 genomes]
rs74128362	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128369	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128371	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128372	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128374	1.00[ASN][1000 genomes]
rs74128384	1.00[ASN][1000 genomes]
rs74128386	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74128391	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008993	chr1:174180019-174331358	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv872553	chr1:174195629-174373379	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv872554	chr1:174209978-174291950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55687343	RC3H1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174202400-174256800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:174211200-174258200	Weak transcription	Dnd41	blood
3	chr1:174213800-174258600	Weak transcription	K562	blood
4	chr1:174214600-174270000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:174223400-174257800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:174232400-174258200	Weak transcription	Gastric	stomach
7	chr1:174232400-174258800	Weak transcription	Aorta	Aorta
8	chr1:174232400-174258800	Weak transcription	Right Ventricle	heart
9	chr1:174232400-174259400	Weak transcription	HSMM	muscle
10	chr1:174232600-174252800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:174232600-174262000	Weak transcription	HMEC	breast
12	chr1:174236000-174259800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:174238200-174261200	Weak transcription	Hela-S3	cervix
14	chr1:174239600-174262400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:174240000-174270600	Weak transcription	Colonic Mucosa	Colon
16	chr1:174241000-174261600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:174241600-174255000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:174242000-174258800	Weak transcription	Brain Germinal Matrix	brain
19	chr1:174242400-174252600	Weak transcription	Fetal Kidney	kidney
20	chr1:174242600-174260000	Weak transcription	NHDF-Ad	bronchial
21	chr1:174242800-174277200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:174243400-174258800	Weak transcription	Esophagus	oesophagus
23	chr1:174243800-174275800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:174244000-174258200	Weak transcription	Fetal Brain Male	brain
25	chr1:174244400-174256600	Weak transcription	Fetal Intestine Large	intestine
26	chr1:174244400-174274000	Weak transcription	Fetal Heart	heart
27	chr1:174246000-174257000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:174246000-174258800	Weak transcription	Thymus	Thymus
29	chr1:174246200-174284200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:174246400-174253200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:174246400-174256400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:174247400-174253800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:174247400-174257800	Weak transcription	Ovary	ovary
34	chr1:174247600-174252200	Strong transcription	GM12878-XiMat	blood
35	chr1:174248000-174259000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:174248000-174259200	Weak transcription	Spleen	Spleen
37	chr1:174248200-174253800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr1:174248200-174262200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:174248600-174253400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:174248600-174258600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:174248800-174265000	Weak transcription	Small Intestine	intestine
42	chr1:174249200-174252200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:174249200-174253400	Strong transcription	Primary T cells from cord blood	blood
44	chr1:174249200-174254600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:174249200-174259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:174249400-174252600	Weak transcription	Fetal Brain Female	brain
47	chr1:174249600-174254600	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:174249800-174262400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:174249800-174270000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:174250000-174255000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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