Variant report

Variant	rs55790393
Chromosome Location	chr19:21506184-21506185
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:21504637..21507576-chr19:21510636..21512879,2	MCF-7	breast:
2	chr19:21496090..21497696-chr19:21505089..21507534,2	K562	blood:
3	chr19:21500655..21502261-chr19:21504561..21506244,2	K562	blood:

Variant related genes	Relation type
ENSG00000182141	Chromatin interaction
ENSG00000268322	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10414834	0.87[EUR][1000 genomes]
rs10424079	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11666213	0.87[EUR][1000 genomes]
rs11666447	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11666525	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11666540	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11667103	0.97[EUR][1000 genomes]
rs11667361	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11667392	0.91[EUR][1000 genomes]
rs11669033	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11669790	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670815	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670868	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11672341	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672583	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11673320	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879901	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13346641	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1621154	0.97[EUR][1000 genomes]
rs1626404	0.97[EUR][1000 genomes]
rs1762578	0.97[EUR][1000 genomes]
rs17680605	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1781867	0.97[EUR][1000 genomes]
rs1781872	0.97[EUR][1000 genomes]
rs1967182	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2061916	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2154302	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2358993	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2359144	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2359145	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2562405	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562411	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2562413	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562416	0.86[EUR][1000 genomes]
rs2650776	0.86[EUR][1000 genomes]
rs2650844	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2650848	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs279807	0.92[EUR][1000 genomes]
rs279809	0.92[EUR][1000 genomes]
rs3853837	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3853838	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4321312	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4327181	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4359573	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4544364	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4638726	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55756795	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55875743	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55899865	0.97[EUR][1000 genomes]
rs57299552	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58412280	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60173523	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61035285	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107465	0.95[EUR][1000 genomes]
rs62107468	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62107469	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62107472	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62107479	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62107531	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62107532	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107534	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107536	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62107539	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107540	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107541	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62109225	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62109226	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62109227	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62109228	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62109229	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62110071	0.92[EUR][1000 genomes]
rs62110367	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62110377	0.88[EUR][1000 genomes]
rs62110416	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62110420	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62110424	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62110426	0.91[EUR][1000 genomes]
rs62110428	0.87[EUR][1000 genomes]
rs62110429	0.87[EUR][1000 genomes]
rs7246339	0.97[EUR][1000 genomes]
rs7251135	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7258099	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7258473	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7258562	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73537884	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55790393	ZNF708	cis	lung	GTEx
rs55790393	ZNF708	cis	Muscle Skeletal	GTEx
rs55790393	RP11-678G14.2	cis	Whole Blood	GTEx
rs55790393	ZNF708	cis	Thyroid	GTEx
rs55790393	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
2	chr19:21474800-21509800	Weak transcription	Fetal Brain Male	brain
3	chr19:21475200-21511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:21484400-21511000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:21485400-21508600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:21485400-21511200	Weak transcription	Gastric	stomach
7	chr19:21487600-21508600	Weak transcription	Fetal Kidney	kidney
8	chr19:21487600-21511200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:21488200-21511200	Weak transcription	Aorta	Aorta
10	chr19:21489000-21510800	Weak transcription	NH-A	brain
11	chr19:21489600-21509000	Weak transcription	Placenta	Placenta
12	chr19:21490200-21508800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:21490200-21509200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:21492400-21506200	Weak transcription	Fetal Lung	lung
15	chr19:21492400-21508600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr19:21492400-21508800	Weak transcription	Fetal Intestine Large	intestine
17	chr19:21492400-21509000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:21492600-21509000	Weak transcription	Fetal Muscle Leg	muscle
19	chr19:21492800-21506600	Weak transcription	Fetal Thymus	thymus
20	chr19:21493000-21509200	Weak transcription	Fetal Intestine Small	intestine
21	chr19:21495400-21508400	Weak transcription	Fetal Brain Female	brain
22	chr19:21496800-21509800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:21497400-21508600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
24	chr19:21497600-21511000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:21498000-21506800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:21498400-21510600	Weak transcription	HUVEC	blood vessel
27	chr19:21498400-21511200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:21498800-21510400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:21500000-21509400	Weak transcription	Fetal Stomach	stomach
30	chr19:21500400-21506200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:21500600-21506200	ZNF genes & repeats	GM12878-XiMat	blood
32	chr19:21500600-21509000	Weak transcription	Primary T cells from cord blood	blood
33	chr19:21500800-21506800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr19:21501000-21506600	Enhancers	Brain Substantia Nigra	brain
35	chr19:21501000-21508800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr19:21501000-21508800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:21501000-21509000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:21501000-21509000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr19:21501000-21509000	Weak transcription	HSMM	muscle
40	chr19:21501000-21509400	Weak transcription	Esophagus	oesophagus
41	chr19:21501000-21510600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:21501000-21511200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr19:21501000-21511200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:21501000-21511200	Weak transcription	Psoas Muscle	Psoas
45	chr19:21501200-21506200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:21501200-21508600	Weak transcription	A549	lung
47	chr19:21501200-21508800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:21501200-21510800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:21501600-21506200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr19:21501600-21506600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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