Variant report

Variant	rs16996102
Chromosome Location	chr19:19562207-19562208
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19561513..19563925-chr19:19567035..19569064,2	K562	blood:
2	chr19:19495316..19499202-chr19:19560908..19564749,3	K562	blood:
3	chr19:19559572..19562278-chr19:19567479..19570303,3	MCF-7	breast:
4	chr19:19561186..19563740-chr19:19587907..19590423,2	K562	blood:
5	chr19:19550732..19553688-chr19:19561837..19563722,2	MCF-7	breast:
6	chr19:19524155..19525700-chr19:19561658..19564532,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10401822	1.00[AMR][1000 genomes]
rs10403737	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405475	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412351	0.89[AFR][1000 genomes]
rs10413582	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416335	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417715	0.94[YRI][hapmap]
rs10421166	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423535	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425574	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13344439	0.89[AMR][1000 genomes]
rs16996031	0.89[YRI][hapmap]
rs16996042	0.94[YRI][hapmap]
rs55927831	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59344441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60455087	0.89[AMR][1000 genomes]
rs73922887	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922890	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922895	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922896	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9304961	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19522200-19563400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:19540200-19562600	Weak transcription	Fetal Intestine Large	intestine
3	chr19:19544400-19563400	Weak transcription	Fetal Kidney	kidney
4	chr19:19545600-19568600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:19545800-19563400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:19545800-19568600	Weak transcription	Brain Substantia Nigra	brain
7	chr19:19545800-19570600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:19546000-19566600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:19546200-19569000	Weak transcription	Colon Smooth Muscle	Colon
10	chr19:19550400-19562400	Weak transcription	A549	lung
11	chr19:19551000-19571200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:19553000-19563000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr19:19553400-19564400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr19:19553400-19564800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr19:19554000-19564000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:19554200-19564600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr19:19555200-19565800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:19556000-19567400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:19556200-19563000	Weak transcription	Aorta	Aorta
20	chr19:19556200-19567400	Weak transcription	Osteobl	bone
21	chr19:19557400-19567200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:19557600-19568600	Weak transcription	HUVEC	blood vessel
23	chr19:19557600-19569000	Weak transcription	NH-A	brain
24	chr19:19557800-19564000	Enhancers	Left Ventricle	heart
25	chr19:19557800-19567400	Weak transcription	HepG2	liver
26	chr19:19557800-19569400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:19558000-19564400	Enhancers	Fetal Muscle Trunk	muscle
28	chr19:19558200-19564400	Enhancers	Fetal Muscle Leg	muscle
29	chr19:19558200-19567000	Weak transcription	Dnd41	blood
30	chr19:19558200-19567000	Weak transcription	Hela-S3	cervix
31	chr19:19558200-19571400	Weak transcription	Brain Germinal Matrix	brain
32	chr19:19558400-19568600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:19558600-19567400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:19558600-19570400	Weak transcription	HMEC	breast
35	chr19:19558800-19567000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:19558800-19567000	Weak transcription	HSMMtube	muscle
37	chr19:19558800-19568800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:19558800-19569600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr19:19559000-19563000	Weak transcription	Stomach Mucosa	stomach
40	chr19:19559000-19566600	Weak transcription	Placenta	Placenta
41	chr19:19559000-19567000	Weak transcription	NHLF	lung
42	chr19:19559000-19567400	Weak transcription	HSMM	muscle
43	chr19:19559000-19567600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr19:19559000-19567600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr19:19559000-19568600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:19559000-19569200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:19559200-19562400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:19559200-19562600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:19559200-19562800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:19559200-19563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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