Variant report

Variant	rs7253821
Chromosome Location	chr19:19784891-19784892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19779580..19781549-chr19:19783005..19784899,2	K562	blood:
2	chr19:19779640..19782271-chr19:19782688..19785412,3	MCF-7	breast:
3	chr19:19784664..19786349-chr19:19788589..19791062,2	K562	blood:

Variant related genes	Relation type
ENSG00000181896	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10401926	1.00[ASW][hapmap];0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10403579	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10415278	0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10421328	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10423449	0.94[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11668721	0.94[CEU][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11669730	1.00[CHD][hapmap]
rs11671684	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12977072	1.00[CHD][hapmap]
rs2288865	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs2288867	0.83[TSI][hapmap]
rs34174818	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55831814	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56236407	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73006705	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8108180	1.00[CHD][hapmap]
rs8110126	1.00[CHD][hapmap]
rs867616	0.94[CEU][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs884480	0.94[CEU][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs919778	0.82[CEU][hapmap]

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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv911310	chr19:19753882-19784891	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7253821	SNORA68	cis	parietal	SCAN
rs7253821	ZNF101	cis	parietal	SCAN
rs7253821	C21orf128	trans	cerebellum	SCAN
rs7253821	ZNF14	cis	parietal	SCAN
rs7253821	ZNF14	cis	cerebellum	SCAN
rs7253821	C19orf60	cis	parietal	SCAN
rs7253821	ZNF714	cis	parietal	SCAN
rs7253821	GMIP	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19780000-19785600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr19:19780200-19786400	Weak transcription	Ovary	ovary
3	chr19:19780200-19788200	Weak transcription	Aorta	Aorta
4	chr19:19780200-19789800	Weak transcription	Fetal Brain Male	brain
5	chr19:19780200-19790000	Weak transcription	Fetal Heart	heart
6	chr19:19780600-19788800	Weak transcription	Fetal Kidney	kidney
7	chr19:19780600-19788800	Weak transcription	HSMMtube	muscle
8	chr19:19780600-19790000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:19780600-19795000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:19780800-19787800	Weak transcription	NHDF-Ad	bronchial
11	chr19:19780800-19788200	Weak transcription	HUVEC	blood vessel
12	chr19:19780800-19789800	Weak transcription	Psoas Muscle	Psoas
13	chr19:19780800-19790000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:19780800-19795000	ZNF genes & repeats	Fetal Thymus	thymus
15	chr19:19780800-19795000	ZNF genes & repeats	Thymus	Thymus
16	chr19:19781000-19785000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:19781000-19785000	Weak transcription	A549	lung
18	chr19:19781000-19785200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr19:19781000-19786000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr19:19781000-19786400	Weak transcription	Fetal Muscle Leg	muscle
21	chr19:19781000-19787000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:19781000-19787800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:19781000-19788000	Weak transcription	Brain Anterior Caudate	brain
24	chr19:19781000-19788200	Weak transcription	Brain Angular Gyrus	brain
25	chr19:19781000-19788200	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:19781000-19788200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:19781000-19788400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:19781000-19788400	Weak transcription	Fetal Lung	lung
29	chr19:19781000-19788400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr19:19781000-19789600	Weak transcription	Fetal Brain Female	brain
31	chr19:19781000-19789800	Weak transcription	Brain Substantia Nigra	brain
32	chr19:19781000-19792600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:19781200-19785000	Weak transcription	HMEC	breast
34	chr19:19781200-19785400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr19:19781200-19786000	Weak transcription	Small Intestine	intestine
36	chr19:19781200-19786200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:19781200-19786200	Weak transcription	Adipose Nuclei	Adipose
38	chr19:19781200-19786200	Weak transcription	HSMM	muscle
39	chr19:19781200-19786200	Weak transcription	K562	blood
40	chr19:19781200-19786400	Weak transcription	NH-A	brain
41	chr19:19781200-19787800	Weak transcription	Hela-S3	cervix
42	chr19:19781200-19787800	Weak transcription	Osteobl	bone
43	chr19:19781200-19788000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:19781200-19788200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:19781200-19788200	Weak transcription	Stomach Mucosa	stomach
46	chr19:19781200-19789800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr19:19781200-19790000	Weak transcription	Colon Smooth Muscle	Colon
48	chr19:19781200-19795800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr19:19781400-19786800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr19:19781400-19788000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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