Variant report

Variant	rs1621154
Chromosome Location	chr19:21483581-21483582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21482877..21485011-chr19:21492555..21495180,2	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10414834	0.87[EUR][1000 genomes]
rs10424079	0.83[EUR][1000 genomes]
rs11666213	0.87[EUR][1000 genomes]
rs11666447	0.91[EUR][1000 genomes]
rs11666525	0.91[EUR][1000 genomes]
rs11666540	0.97[EUR][1000 genomes]
rs11667103	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667361	0.97[EUR][1000 genomes]
rs11667392	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669033	0.91[EUR][1000 genomes]
rs11669790	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670815	0.97[EUR][1000 genomes]
rs11670868	0.88[EUR][1000 genomes]
rs11672341	0.98[EUR][1000 genomes]
rs11672583	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673320	0.87[EUR][1000 genomes]
rs11879901	0.97[EUR][1000 genomes]
rs13346641	0.83[EUR][1000 genomes]
rs1626404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1762578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680605	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781867	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781872	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967182	0.81[EUR][1000 genomes]
rs2061916	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154302	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2358993	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359144	0.83[EUR][1000 genomes]
rs2359145	0.91[EUR][1000 genomes]
rs2562405	0.83[EUR][1000 genomes]
rs2562411	0.81[EUR][1000 genomes]
rs2562413	0.83[EUR][1000 genomes]
rs2562416	0.86[EUR][1000 genomes]
rs2650776	0.86[EUR][1000 genomes]
rs2650844	0.83[EUR][1000 genomes]
rs2650848	0.83[EUR][1000 genomes]
rs279807	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279809	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853837	0.89[EUR][1000 genomes]
rs3853838	0.89[EUR][1000 genomes]
rs4321312	0.97[EUR][1000 genomes]
rs4327181	0.95[EUR][1000 genomes]
rs4359573	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544364	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638726	0.85[EUR][1000 genomes]
rs516519	0.80[EUR][1000 genomes]
rs55756795	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55790393	0.97[EUR][1000 genomes]
rs55875743	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55899865	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57299552	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58412280	0.92[EUR][1000 genomes]
rs60173523	0.92[EUR][1000 genomes]
rs61035285	0.97[EUR][1000 genomes]
rs62107465	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107468	0.89[EUR][1000 genomes]
rs62107469	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107472	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62107479	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107531	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107532	0.98[EUR][1000 genomes]
rs62107534	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107536	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107539	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107540	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107541	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109225	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109226	0.93[EUR][1000 genomes]
rs62109227	0.87[EUR][1000 genomes]
rs62109228	0.87[EUR][1000 genomes]
rs62109229	0.97[EUR][1000 genomes]
rs62110071	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110367	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62110377	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110416	0.91[EUR][1000 genomes]
rs62110420	0.91[EUR][1000 genomes]
rs62110424	0.91[EUR][1000 genomes]
rs62110426	0.91[EUR][1000 genomes]
rs62110428	0.87[EUR][1000 genomes]
rs62110429	0.87[EUR][1000 genomes]
rs627522	0.80[EUR][1000 genomes]
rs7246339	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251135	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258099	0.97[EUR][1000 genomes]
rs7258473	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258562	0.95[EUR][1000 genomes]
rs73537884	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv911415	chr19:21388995-21487170	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv911419	chr19:21391844-21487170	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1621154	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs1621154	ZNF708	cis	Muscle Skeletal	GTEx
rs1621154	RP11-678G14.2	cis	Esophagus Muscularis	GTEx
rs1621154	RP11-678G14.2	cis	Whole Blood	GTEx
rs1621154	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs1621154	ZNF708	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21465400-21484600	ZNF genes & repeats	Liver	Liver
3	chr19:21467200-21489600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:21470600-21484200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
5	chr19:21472200-21487600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:21472200-21490400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:21473600-21487200	Weak transcription	Right Ventricle	heart
8	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
9	chr19:21474000-21490600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr19:21474400-21492400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:21474800-21509800	Weak transcription	Fetal Brain Male	brain
12	chr19:21475200-21483600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:21475200-21484000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:21475200-21484200	Weak transcription	Fetal Thymus	thymus
15	chr19:21475200-21485400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:21475200-21511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:21476000-21490400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
18	chr19:21476000-21490400	Weak transcription	Hela-S3	cervix
19	chr19:21476200-21488200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:21476800-21487200	Weak transcription	Brain Angular Gyrus	brain
21	chr19:21476800-21497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:21477000-21494400	Weak transcription	Stomach Mucosa	stomach
23	chr19:21477200-21495000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr19:21477400-21483800	Weak transcription	Brain Anterior Caudate	brain
25	chr19:21477600-21484200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr19:21477600-21484400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr19:21477600-21495800	Weak transcription	HepG2	liver
28	chr19:21478000-21484200	Weak transcription	Brain Germinal Matrix	brain
29	chr19:21478000-21484200	Weak transcription	Colonic Mucosa	Colon
30	chr19:21478000-21497400	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:21478200-21483600	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:21478200-21483600	Weak transcription	Fetal Brain Female	brain
33	chr19:21478200-21487000	Weak transcription	Brain Substantia Nigra	brain
34	chr19:21478200-21487200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:21478200-21492600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr19:21478400-21500600	Weak transcription	Psoas Muscle	Psoas
37	chr19:21478600-21483800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr19:21478600-21484000	Weak transcription	Fetal Kidney	kidney
39	chr19:21478600-21490600	Strong transcription	Fetal Lung	lung
40	chr19:21478600-21499200	Weak transcription	HMEC	breast
41	chr19:21478800-21484200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:21479200-21483600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr19:21479200-21484000	Weak transcription	Gastric	stomach
44	chr19:21479400-21483800	Weak transcription	Osteobl	bone
45	chr19:21480000-21484400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
46	chr19:21480400-21486000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:21480400-21487800	Strong transcription	Adipose Nuclei	Adipose
48	chr19:21480600-21483800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr19:21480600-21485400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:21480600-21487800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links