Variant report

Variant	rs241936
Chromosome Location	chr19:38310886-38310887
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38310273..38312700-chr19:38313306..38315862,2	MCF-7	breast:

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L3-3	chr19:38310864-38310935	ENSG00000267640.1
2	lnc-SIPA1L3-3	chr19:38310864-38310946	NONHSAT066164
3	lnc-SIPA1L3-3	chr19:38310864-38310946	ENSG00000267640.1
4	lnc-SIPA1L3-3	chr19:38310864-38310946	ENSG00000267640.1
5	lnc-SIPA1L3-3	chr19:38310864-38310946	ENSG00000267640.1
6	lnc-SIPA1L3-3	chr19:38310864-38314365	NONHSAT066169
7	lnc-SIPA1L3-3	chr19:38310864-38310946	ENSG00000267640.1

No data

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs2216299	1.00[AMR][1000 genomes]
rs2248576	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2385006	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs241934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs241938	1.00[AMR][1000 genomes]
rs241939	1.00[AMR][1000 genomes]
rs241945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs241958	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs241961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2891656	1.00[AMR][1000 genomes]
rs2909087	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909089	1.00[AMR][1000 genomes]
rs2909090	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909091	1.00[AMR][1000 genomes]
rs2909094	1.00[AMR][1000 genomes]
rs2909095	1.00[AMR][1000 genomes]
rs2909096	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909099	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909101	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909107	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972429	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972431	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972432	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972433	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972435	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972436	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972440	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972441	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972443	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972450	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972451	1.00[AMR][1000 genomes]
rs2972460	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3095723	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3095725	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3112436	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34301943	1.00[AMR][1000 genomes]
rs59246699	1.00[AMR][1000 genomes]
rs61744939	1.00[AMR][1000 genomes]
rs6508740	1.00[AMR][1000 genomes]
rs7245750	1.00[AMR][1000 genomes]
rs7249524	1.00[AMR][1000 genomes]
rs7251623	1.00[AMR][1000 genomes]
rs7252424	1.00[AMR][1000 genomes]
rs7259281	1.00[AMR][1000 genomes]
rs8106132	1.00[AMR][1000 genomes]
rs856294	1.00[AMR][1000 genomes]
rs856296	1.00[AMR][1000 genomes]
rs856297	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs856303	1.00[AMR][1000 genomes]
rs978723	1.00[AMR][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	chr19:38308600-38312000	Weak transcription	Aorta	Aorta
2	chr19:38308600-38314800	Weak transcription	Gastric	stomach
3	chr19:38308800-38311600	Weak transcription	Colon Smooth Muscle	Colon
4	chr19:38308800-38311800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:38308800-38312000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:38308800-38312000	Weak transcription	Fetal Intestine Large	intestine
7	chr19:38308800-38312200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr19:38308800-38312200	Weak transcription	Left Ventricle	heart
9	chr19:38308800-38313200	Weak transcription	Esophagus	oesophagus
10	chr19:38308800-38314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:38308800-38314400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:38308800-38314400	Weak transcription	Brain Angular Gyrus	brain
13	chr19:38308800-38314400	Weak transcription	Fetal Muscle Leg	muscle
14	chr19:38308800-38314400	Weak transcription	Right Ventricle	heart
15	chr19:38308800-38314600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:38308800-38314600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr19:38308800-38314600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr19:38308800-38315400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:38309000-38311400	Weak transcription	Fetal Kidney	kidney
20	chr19:38309000-38312000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:38309000-38313000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:38309000-38313200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:38309000-38314200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:38309000-38314200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr19:38309000-38314600	Weak transcription	Fetal Heart	heart
26	chr19:38309000-38316800	Weak transcription	Stomach Mucosa	stomach
27	chr19:38309400-38315000	Weak transcription	Placenta	Placenta
28	chr19:38309600-38314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr19:38309600-38319200	ZNF genes & repeats	Fetal Brain Female	brain
30	chr19:38310000-38312000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr19:38310000-38312400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr19:38310000-38317000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr19:38310000-38317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:38310000-38318200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:38310200-38311000	ZNF genes & repeats	Brain Germinal Matrix	brain
36	chr19:38310200-38311000	Strong transcription	Brain Substantia Nigra	brain
37	chr19:38310200-38311600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr19:38310200-38312000	Strong transcription	Pancreatic Islets	Pancreatic Islet
39	chr19:38310200-38312000	Strong transcription	Ovary	ovary
40	chr19:38310200-38312600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:38310200-38313800	ZNF genes & repeats	Fetal Brain Male	brain
42	chr19:38310200-38317600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr19:38310400-38311000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
44	chr19:38310400-38312800	Strong transcription	Brain Hippocampus Middle	brain
45	chr19:38310600-38311200	ZNF genes & repeats	Fetal Stomach	stomach
46	chr19:38310600-38315000	Weak transcription	Pancreas	Pancrea
47	chr19:38310800-38312000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:38310800-38312400	Strong transcription	Brain Anterior Caudate	brain
49	chr19:38310800-38313600	ZNF genes & repeats	Adipose Nuclei	Adipose
50	chr19:38310800-38314000	Strong transcription	Fetal Lung	lung

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