Variant report

Variant	rs16975884
Chromosome Location	chr19:38313578-38313579
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	chr19:38310273..38312700-chr19:38313306..38315862,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L3-3	chr19:38310864-38314365	NONHSAT066169

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11878261	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11880056	1.00[CEU][hapmap]
rs11883255	1.00[CEU][hapmap]
rs16975881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110187	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62110188	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62110190	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110192	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110193	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62110194	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110217	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62110222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110229	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62110230	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62110232	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62112272	0.93[AMR][1000 genomes]
rs62112273	0.93[AMR][1000 genomes]
rs7245965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245981	1.00[CEU][hapmap]
rs7246147	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7247345	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7251502	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7258680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8100469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105754	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38308600-38314800	Weak transcription	Gastric	stomach
2	chr19:38308800-38314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:38308800-38314400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:38308800-38314400	Weak transcription	Brain Angular Gyrus	brain
5	chr19:38308800-38314400	Weak transcription	Fetal Muscle Leg	muscle
6	chr19:38308800-38314400	Weak transcription	Right Ventricle	heart
7	chr19:38308800-38314600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:38308800-38314600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr19:38308800-38314600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr19:38308800-38315400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr19:38309000-38314200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr19:38309000-38314200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:38309000-38314600	Weak transcription	Fetal Heart	heart
14	chr19:38309000-38316800	Weak transcription	Stomach Mucosa	stomach
15	chr19:38309400-38315000	Weak transcription	Placenta	Placenta
16	chr19:38309600-38314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:38309600-38319200	ZNF genes & repeats	Fetal Brain Female	brain
18	chr19:38310000-38317000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:38310000-38317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:38310000-38318200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:38310200-38313800	ZNF genes & repeats	Fetal Brain Male	brain
22	chr19:38310200-38317600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr19:38310600-38315000	Weak transcription	Pancreas	Pancrea
24	chr19:38310800-38313600	ZNF genes & repeats	Adipose Nuclei	Adipose
25	chr19:38310800-38314000	Strong transcription	Fetal Lung	lung
26	chr19:38311000-38313800	Weak transcription	Brain Substantia Nigra	brain
27	chr19:38311000-38314400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:38311400-38314600	Weak transcription	Fetal Stomach	stomach
29	chr19:38312000-38315000	Strong transcription	Fetal Intestine Large	intestine
30	chr19:38312000-38317400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
31	chr19:38312000-38317800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
32	chr19:38312000-38317800	ZNF genes & repeats	Ovary	ovary
33	chr19:38312000-38318400	ZNF genes & repeats	Brain Germinal Matrix	brain
34	chr19:38312000-38324000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
35	chr19:38312200-38313600	Strong transcription	Left Ventricle	heart
36	chr19:38312200-38314400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr19:38312400-38313600	ZNF genes & repeats	Brain Anterior Caudate	brain
38	chr19:38312400-38313800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
39	chr19:38312400-38314400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr19:38312400-38314400	Weak transcription	Fetal Kidney	kidney
41	chr19:38312600-38315000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr19:38312800-38314600	Weak transcription	Brain Hippocampus Middle	brain
43	chr19:38312800-38316000	ZNF genes & repeats	Liver	Liver
44	chr19:38313000-38318800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
45	chr19:38313200-38315600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:38313200-38317800	ZNF genes & repeats	Colon Smooth Muscle	Colon
47	chr19:38313400-38314400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:38313400-38314600	Weak transcription	Aorta	Aorta
49	chr19:38313400-38314600	Weak transcription	Esophagus	oesophagus
50	chr19:38313400-38314600	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links