Variant report

Variant	rs28377909
Chromosome Location	chr19:39161438-39161439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39160838..39163402-chr19:39174691..39176835,2	MCF-7	breast:
2	chr19:39156222..39158028-chr19:39160453..39162596,3	K562	blood:
3	chr19:39152656..39156169-chr19:39159383..39162487,4	K562	blood:
4	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
5	chr19:39161055..39163275-chr19:39172924..39175598,3	K562	blood:
6	chr19:39156254..39158028-chr19:39160745..39162596,2	K562	blood:
7	chr19:39161163..39163302-chr19:39198153..39200836,2	K562	blood:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10424568	0.81[EUR][1000 genomes]
rs10426809	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11083473	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	nsv960837	chr19:39156364-39162333	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39152600-39162200	Enhancers	Spleen	Spleen
3	chr19:39152600-39164000	Enhancers	Liver	Liver
4	chr19:39154000-39162600	Enhancers	Fetal Kidney	kidney
5	chr19:39154000-39162800	Enhancers	Small Intestine	intestine
6	chr19:39154200-39162600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr19:39154600-39162000	Enhancers	Left Ventricle	heart
8	chr19:39154600-39163000	Enhancers	Right Atrium	heart
9	chr19:39154800-39163000	Genic enhancers	Fetal Intestine Small	intestine
10	chr19:39155000-39162800	Genic enhancers	Fetal Intestine Large	intestine
11	chr19:39155200-39162800	Enhancers	Brain Angular Gyrus	brain
12	chr19:39155200-39163800	Genic enhancers	NHEK	skin
13	chr19:39155400-39162800	Enhancers	Brain Hippocampus Middle	brain
14	chr19:39155400-39162800	Enhancers	Brain Substantia Nigra	brain
15	chr19:39155800-39162400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr19:39156000-39162200	Enhancers	NHDF-Ad	bronchial
17	chr19:39156000-39162800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:39156400-39162800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:39156600-39164800	Enhancers	Fetal Heart	heart
20	chr19:39157800-39162600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr19:39157800-39162600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr19:39158000-39161800	Enhancers	Fetal Thymus	thymus
23	chr19:39158000-39162000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:39158000-39162800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr19:39158200-39162800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr19:39158200-39162800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr19:39158400-39162600	Genic enhancers	HMEC	breast
28	chr19:39158600-39162600	Enhancers	Primary B cells from peripheral blood	blood
29	chr19:39158600-39162800	Genic enhancers	Osteobl	bone
30	chr19:39158800-39162800	Enhancers	Adipose Nuclei	Adipose
31	chr19:39158800-39162800	Enhancers	Colon Smooth Muscle	Colon
32	chr19:39158800-39167600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:39159000-39165000	Weak transcription	Hela-S3	cervix
34	chr19:39159000-39166600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:39159000-39166800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:39159200-39162600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:39159400-39162800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:39159600-39162800	Enhancers	H1 Cell Line	embryonic stem cell
39	chr19:39159600-39162800	Enhancers	Aorta	Aorta
40	chr19:39159600-39162800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr19:39159600-39169600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:39160000-39162200	Enhancers	Fetal Lung	lung
43	chr19:39160000-39162800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:39160000-39162800	Enhancers	Brain Cingulate Gyrus	brain
45	chr19:39160000-39162800	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr19:39160200-39162800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:39160400-39161600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:39160400-39162200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:39160400-39162800	Enhancers	H9 Cell Line	embryonic stem cell
50	chr19:39160400-39162800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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