Variant report

Variant	rs8109835
Chromosome Location	chr19:38422223-38422224
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr19:38422209-38425183	A549	lung:	n/a	chr19:38424431-38424440 chr19:38423719-38423728
2	FOSL2	chr19:38422174-38424966	A549	lung:	n/a	chr19:38423719-38423728 chr19:38424431-38424440 chr19:38423719-38423727 chr19:38423720-38423727 chr19:38424430-38424439
3	TCF12	chr19:38421072-38425291	A549	lung:	n/a	chr19:38421714-38421722
4	REST	chr19:38422035-38423605	A549	lung:	n/a	n/a
5	GATA3	chr19:38422214-38425343	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:
3	chr19:38420982..38422890-chr19:38471015..38472804,2	MCF-7	breast:
4	chr19:38396701..38399337-chr19:38419695..38422490,2	K562	blood:

Variant related genes	Relation type
SIPA1L3	TF binding region
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10404159	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415399	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10415548	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083441	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12608883	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12973580	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1643460	0.82[EUR][1000 genomes]
rs1643461	0.86[EUR][1000 genomes]
rs1725499	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28460297	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353410	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs353411	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3786869	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4239516	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802144	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802147	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802151	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803551	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803573	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705491	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705493	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705495	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705499	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8108434	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109053	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113273	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8113521	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic 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	5 gene(s)	inside rSNPs	diseases
3	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv960761	chr19:38419928-38422738	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
2	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:38399000-38422400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:38399200-38422400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
6	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
9	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:38399800-38422400	Weak transcription	Fetal Brain Female	brain
11	chr19:38399800-38422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr19:38400600-38422400	Weak transcription	HUVEC	blood vessel
13	chr19:38400800-38422400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr19:38402000-38422600	Weak transcription	Fetal Brain Male	brain
15	chr19:38405200-38422600	Weak transcription	Right Ventricle	heart
16	chr19:38405600-38422800	Weak transcription	Colon Smooth Muscle	Colon
17	chr19:38406000-38422600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:38410200-38422400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr19:38410400-38422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:38411600-38422600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:38411800-38422600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:38412000-38422600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr19:38412000-38423800	Weak transcription	Lung	lung
25	chr19:38412200-38422600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr19:38412200-38422800	Weak transcription	Adipose Nuclei	Adipose
27	chr19:38412200-38423000	Weak transcription	Thymus	Thymus
28	chr19:38417600-38422600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:38417600-38422600	Weak transcription	Ovary	ovary
30	chr19:38418200-38422400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:38418600-38422400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr19:38418600-38422400	Enhancers	Fetal Intestine Large	intestine
33	chr19:38418600-38422600	Enhancers	Primary hematopoietic stem cells	blood
34	chr19:38418800-38422600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:38418800-38425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:38419200-38422400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr19:38419400-38422400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr19:38419400-38424800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:38419600-38422400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr19:38419600-38422400	Weak transcription	Psoas Muscle	Psoas
41	chr19:38419600-38422600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:38419800-38422400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:38419800-38422400	Enhancers	HepG2	liver
44	chr19:38419800-38422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:38419800-38422800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:38419800-38422800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:38420000-38422400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr19:38420200-38422400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:38420200-38422600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr19:38420200-38422600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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