Variant report

Variant	rs2749735
Chromosome Location	chr1:93624139-93624140
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93617900..93619477-chr1:93623441..93625211,2	K562	blood:
2	chr1:93623277..93625367-chr1:93644361..93646842,2	MCF-7	breast:
3	chr1:93621616..93625921-chr1:93644666..93648341,4	K562	blood:
4	chr1:93617900..93619581-chr1:93623441..93626747,4	K562	blood:

Variant related genes	Relation type
ENSG00000117500	Chromatin interaction
ENSG00000122483	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1000606	0.80[EUR][1000 genomes]
rs10430073	0.80[EUR][1000 genomes]
rs10782958	0.82[EUR][1000 genomes]
rs10874765	0.82[EUR][1000 genomes]
rs10874767	0.82[EUR][1000 genomes]
rs10874771	0.82[EUR][1000 genomes]
rs11164874	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11164878	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11164882	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11164888	0.82[EUR][1000 genomes]
rs11164889	0.82[EUR][1000 genomes]
rs11164890	0.82[EUR][1000 genomes]
rs11164906	0.80[EUR][1000 genomes]
rs11582703	0.82[EUR][1000 genomes]
rs11584466	0.80[EUR][1000 genomes]
rs11586323	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12057476	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12064785	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12066315	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12067005	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12070900	0.82[EUR][1000 genomes]
rs12071627	0.82[EUR][1000 genomes]
rs12080715	0.82[EUR][1000 genomes]
rs12085959	0.82[EUR][1000 genomes]
rs12087466	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12088338	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12090723	0.82[EUR][1000 genomes]
rs12094547	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12731675	0.82[EUR][1000 genomes]
rs12731809	0.82[EUR][1000 genomes]
rs1414367	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1535698	0.82[EUR][1000 genomes]
rs17131699	0.92[EUR][1000 genomes]
rs2031224	0.80[EUR][1000 genomes]
rs2104280	0.81[EUR][1000 genomes]
rs2391227	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2484485	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2783492	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2783498	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2783506	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2815408	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815409	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815410	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815411	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815412	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2815413	0.90[EUR][1000 genomes]
rs2815414	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36057148	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4573531	0.82[EUR][1000 genomes]
rs4847407	0.81[EUR][1000 genomes]
rs4847409	0.80[EUR][1000 genomes]
rs485622	0.83[EUR][1000 genomes]
rs504810	0.81[EUR][1000 genomes]
rs505531	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs506556	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs512361	0.80[EUR][1000 genomes]
rs519723	0.82[EUR][1000 genomes]
rs522999	0.90[EUR][1000 genomes]
rs546	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs556888	0.80[EUR][1000 genomes]
rs55701931	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs558667	0.82[EUR][1000 genomes]
rs559397	0.82[EUR][1000 genomes]
rs56303209	0.82[EUR][1000 genomes]
rs571212	0.83[EUR][1000 genomes]
rs573056	0.88[EUR][1000 genomes]
rs581825	0.89[EUR][1000 genomes]
rs587754	0.82[EUR][1000 genomes]
rs605759	0.84[EUR][1000 genomes]
rs615416	0.90[EUR][1000 genomes]
rs626714	0.82[EUR][1000 genomes]
rs629153	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs631966	0.80[EUR][1000 genomes]
rs633789	0.80[EUR][1000 genomes]
rs6541400	0.80[EUR][1000 genomes]
rs658178	0.80[AFR][1000 genomes]
rs658877	0.90[EUR][1000 genomes]
rs661566	0.81[EUR][1000 genomes]
rs662546	0.81[EUR][1000 genomes]
rs6657587	0.82[EUR][1000 genomes]
rs6667701	0.82[EUR][1000 genomes]
rs667680	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6687359	0.80[EUR][1000 genomes]
rs670650	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs671559	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs693872	0.80[EUR][1000 genomes]
rs71510760	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7413775	0.80[EUR][1000 genomes]
rs7519163	0.80[EUR][1000 genomes]
rs7525189	0.80[EUR][1000 genomes]
rs7551635	0.82[EUR][1000 genomes]
rs7555292	0.82[EUR][1000 genomes]
rs797660	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs797669	0.80[EUR][1000 genomes]
rs809515	0.83[EUR][1000 genomes]
rs9432700	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS 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 target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2749735	RP4-717I23.3	cis	Thyroid	GTEx
rs2749735	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2749735	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs2749735	RP4-717I23.3	cis	Artery Aorta	GTEx
rs2749735	RP4-717I23.3	cis	Whole Blood	GTEx
rs2749735	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs2749735	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs2749735	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs2749735	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs2749735	RP4-717I23.3	cis	Stomach	GTEx
rs2749735	RP4-717I23.3	cis	lung	GTEx
rs2749735	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs2749735	RP4-717I23.3	cis	Artery Tibial	GTEx
rs2749735	RP4-717I23.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
2	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
4	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:93582400-93642800	Weak transcription	Gastric	stomach
6	chr1:93583200-93628800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
8	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
9	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:93597400-93625400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
12	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
13	chr1:93601400-93635400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:93602600-93624200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:93602600-93628800	Weak transcription	Aorta	Aorta
16	chr1:93602600-93630200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:93602600-93630200	Weak transcription	Brain Anterior Caudate	brain
18	chr1:93603400-93624600	Weak transcription	Brain Substantia Nigra	brain
19	chr1:93603600-93629200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:93606800-93635400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:93609000-93627400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:93611200-93626200	Strong transcription	Fetal Thymus	thymus
24	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:93613000-93626000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:93613000-93626000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr1:93613200-93625000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:93613200-93626200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:93613200-93627800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:93613400-93625000	Strong transcription	HSMM	muscle
31	chr1:93613400-93625200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:93613600-93624600	Weak transcription	Fetal Heart	heart
33	chr1:93613600-93625600	Strong transcription	Adipose Nuclei	Adipose
34	chr1:93613600-93625800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:93613800-93625800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:93614000-93625800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:93614000-93626000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:93614000-93626200	Strong transcription	Liver	Liver
39	chr1:93614200-93625800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:93614200-93630200	Weak transcription	Right Atrium	heart
41	chr1:93614200-93634800	Weak transcription	A549	lung
42	chr1:93614400-93625800	Strong transcription	Osteobl	bone
43	chr1:93614400-93627400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:93615200-93630200	Weak transcription	Psoas Muscle	Psoas
45	chr1:93615600-93627000	Weak transcription	Ovary	ovary
46	chr1:93615600-93628400	Weak transcription	Left Ventricle	heart
47	chr1:93615600-93643200	Weak transcription	Fetal Kidney	kidney
48	chr1:93616000-93626400	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:93616800-93624600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:93617000-93624800	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links