Variant report

Variant	rs2305105
Chromosome Location	chr19:38314767-38314768
allele	C/T
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-ZNF573-1	chr19:38314363-38315357	NR_040015
2	lnc-ZNF573-1	chr19:38314362-38315357	ENSG00000225868.2

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10401281	0.84[EUR][1000 genomes]
rs10401880	0.81[EUR][1000 genomes]
rs10420417	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421676	0.86[EUR][1000 genomes]
rs1421677	0.86[EUR][1000 genomes]
rs2068431	0.85[EUR][1000 genomes]
rs2075283	0.84[EUR][1000 genomes]
rs2382623	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs241955	0.88[YRI][hapmap]
rs3848625	0.84[EUR][1000 genomes]
rs3910952	0.85[EUR][1000 genomes]
rs4802150	0.87[EUR][1000 genomes]
rs4803525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803528	0.85[EUR][1000 genomes]
rs6508753	0.82[EUR][1000 genomes]
rs697434	0.87[EUR][1000 genomes]
rs705496	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes]
rs7245864	0.85[EUR][1000 genomes]
rs7257190	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7257688	0.82[EUR][1000 genomes]
rs8105305	0.87[EUR][1000 genomes]
rs8108245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833917	0.82[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap]

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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38308600-38314800	Weak transcription	Gastric	stomach
2	chr19:38308800-38315400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:38309000-38316800	Weak transcription	Stomach Mucosa	stomach
4	chr19:38309400-38315000	Weak transcription	Placenta	Placenta
5	chr19:38309600-38314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:38309600-38319200	ZNF genes & repeats	Fetal Brain Female	brain
7	chr19:38310000-38317000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr19:38310000-38317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:38310000-38318200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:38310200-38317600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:38310600-38315000	Weak transcription	Pancreas	Pancrea
12	chr19:38312000-38315000	Strong transcription	Fetal Intestine Large	intestine
13	chr19:38312000-38317400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
14	chr19:38312000-38317800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr19:38312000-38317800	ZNF genes & repeats	Ovary	ovary
16	chr19:38312000-38318400	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr19:38312000-38324000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr19:38312600-38315000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr19:38312800-38316000	ZNF genes & repeats	Liver	Liver
20	chr19:38313000-38318800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
21	chr19:38313200-38315600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:38313200-38317800	ZNF genes & repeats	Colon Smooth Muscle	Colon
23	chr19:38313800-38315000	Strong transcription	Brain Substantia Nigra	brain
24	chr19:38314000-38321600	ZNF genes & repeats	Fetal Lung	lung
25	chr19:38314200-38315600	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr19:38314200-38318600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
27	chr19:38314400-38315000	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr19:38314400-38315200	Strong transcription	Brain Cingulate Gyrus	brain
29	chr19:38314400-38315400	Strong transcription	Brain Angular Gyrus	brain
30	chr19:38314400-38315600	Strong transcription	Rectal Smooth Muscle	rectum
31	chr19:38314400-38315800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr19:38314400-38315800	ZNF genes & repeats	Right Ventricle	heart
33	chr19:38314400-38316000	ZNF genes & repeats	Brain Anterior Caudate	brain
34	chr19:38314400-38317400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:38314400-38317800	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr19:38314400-38318200	ZNF genes & repeats	Fetal Kidney	kidney
37	chr19:38314400-38319200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
38	chr19:38314400-38324600	ZNF genes & repeats	Adipose Nuclei	Adipose
39	chr19:38314600-38314800	ZNF genes & repeats	Esophagus	oesophagus
40	chr19:38314600-38315200	ZNF genes & repeats	Lung	lung
41	chr19:38314600-38315400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:38314600-38315600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
43	chr19:38314600-38315800	ZNF genes & repeats	Brain Hippocampus Middle	brain
44	chr19:38314600-38315800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
45	chr19:38314600-38315800	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr19:38314600-38316000	ZNF genes & repeats	Fetal Heart	heart
47	chr19:38314600-38317200	ZNF genes & repeats	Aorta	Aorta
48	chr19:38314600-38317600	ZNF genes & repeats	Fetal Stomach	stomach
49	chr19:38314600-38317600	ZNF genes & repeats	Left Ventricle	heart
50	chr19:38314600-38317800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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