Variant report

Variant	rs412350
Chromosome Location	chr6:145852409-145852410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1070517	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1070519	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1070520	0.84[AMR][1000 genomes]
rs10872577	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11155433	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11155435	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11155438	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12205752	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12208019	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12208812	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12211884	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1280275	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1280276	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1509213	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1509214	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1912023	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1935612	0.90[EUR][1000 genomes]
rs2092295	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2092296	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2092297	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2096201	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2103633	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs365747	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs365869	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs367065	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs370112	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs370654	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs371186	0.84[EUR][1000 genomes]
rs372904	0.91[EUR][1000 genomes]
rs376257	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs378937	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs379040	0.91[EUR][1000 genomes]
rs383841	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs385729	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs387376	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs392612	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs398408	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs400329	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs401331	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs401561	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs405206	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs407887	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs408443	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs409553	0.84[EUR][1000 genomes]
rs411785	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs414297	0.91[EUR][1000 genomes]
rs414600	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs418701	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs425999	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs426874	0.83[EUR][1000 genomes]
rs427128	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4332001	0.80[EUR][1000 genomes]
rs4335004	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs434318	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs435671	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs436156	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs436498	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs437147	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs439035	0.84[EUR][1000 genomes]
rs440477	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs441290	0.84[EUR][1000 genomes]
rs443628	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4455694	0.82[AMR][1000 genomes]
rs446031	0.84[EUR][1000 genomes]
rs446362	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs448258	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs450921	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs451108	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs451699	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs453834	0.84[EUR][1000 genomes]
rs4896820	0.84[EUR][1000 genomes]
rs4896821	0.83[EUR][1000 genomes]
rs4896824	0.82[EUR][1000 genomes]
rs4896837	0.82[AMR][1000 genomes]
rs4896838	0.82[AMR][1000 genomes]
rs4896839	0.82[AMR][1000 genomes]
rs621382	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6570692	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6570700	0.82[EUR][1000 genomes]
rs6570708	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6899702	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6899900	0.84[EUR][1000 genomes]
rs6900040	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6901888	0.82[AMR][1000 genomes]
rs6902404	0.83[EUR][1000 genomes]
rs6902410	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6912079	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6913727	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6914203	0.90[EUR][1000 genomes]
rs6915094	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6919684	0.84[EUR][1000 genomes]
rs6923074	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6925594	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6941429	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs697053	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs697054	0.80[AMR][1000 genomes]
rs697055	0.82[AMR][1000 genomes]
rs697056	0.82[AMR][1000 genomes]
rs702304	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs702306	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs702307	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs702317	0.82[AMR][1000 genomes]
rs702318	0.82[AMR][1000 genomes]
rs702319	0.82[AMR][1000 genomes]
rs702320	0.82[AMR][1000 genomes]
rs702324	0.82[AMR][1000 genomes]
rs7746330	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7755253	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7755586	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7755887	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7762536	0.82[EUR][1000 genomes]
rs7772717	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7773939	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs857881	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs864148	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs870491	0.82[EUR][1000 genomes]
rs9322028	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9322029	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9373463	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9373464	0.90[EUR][1000 genomes]
rs9376945	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9376950	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9390336	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9390338	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9399553	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9399555	0.84[EUR][1000 genomes]
rs9399561	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9403726	0.90[EUR][1000 genomes]
rs9403729	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9403730	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9403731	0.90[EUR][1000 genomes]
rs9403734	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9403735	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9497357	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs952405	0.82[EUR][1000 genomes]
rs952406	0.80[EUR][1000 genomes];0.80[ASN][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	nsv886746	chr6:145815949-145920894	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv886747	chr6:145815949-145922777	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1028290	chr6:145819982-145911857	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv886748	chr6:145835917-145911730	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1021041	chr6:145836942-145887333	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1016881	chr6:145840961-145887333	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv538465	chr6:145840961-145887333	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs412350	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145850000-145852600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
2	chr6:145850400-145853200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr6:145850400-145854200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:145850600-145852600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr6:145850800-145854600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:145851000-145853200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
7	chr6:145851200-145853000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:145851400-145853600	Weak transcription	Left Ventricle	heart
9	chr6:145851600-145852600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
10	chr6:145851600-145852600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:145851600-145853600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:145851800-145853200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr6:145851800-145856000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:145852000-145853000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:145852000-145856600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:145852200-145853000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:145852400-145852600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr6:145852400-145852800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
19	chr6:145852400-145852800	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links