Variant report

Variant	rs10417995
Chromosome Location	chr19:19103405-19103406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19103318-19103900	K562	blood:	n/a	n/a
2	POLR2A	chr19:19103385-19103853	K562	blood:	n/a	n/a
3	POLR2A	chr19:19103348-19103765	K562	blood:	n/a	n/a
4	POLR2A	chr19:19103311-19103782	PFSK-1	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19099305..19102487-chr19:19102568..19107094,5	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARMC6-1	chr19:19103397-19104419	ENSG00000245755
2	lnc-ARMC6-1	chr19:19103397-19104419	ENSG00000269131.1

No data

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000269131	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10402553	1.00[EUR][1000 genomes]
rs10403808	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10404077	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10404860	1.00[EUR][1000 genomes]
rs10404879	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405178	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405609	1.00[EUR][1000 genomes]
rs10406282	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406341	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406496	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407260	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407753	0.89[AFR][1000 genomes]
rs10407980	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10408567	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10409265	0.84[AFR][1000 genomes]
rs10409395	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411786	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10412101	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413216	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10414535	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10415998	0.84[AFR][1000 genomes]
rs10416041	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416054	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416240	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416250	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416730	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417310	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417682	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418688	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10419114	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419307	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420479	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420559	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422058	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422079	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422813	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423129	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10426131	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13344769	1.00[EUR][1000 genomes]
rs13344835	0.84[AFR][1000 genomes]
rs13345246	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28369262	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28374656	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28376498	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28380085	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28421315	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28445835	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28477157	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28477961	0.95[AFR][1000 genomes]
rs28507927	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28533991	0.82[AFR][1000 genomes]
rs28568599	1.00[EUR][1000 genomes]
rs28582808	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28619464	0.91[AFR][1000 genomes]
rs28628081	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28720008	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35646935	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57654710	1.00[EUR][1000 genomes]
rs6511012	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7252085	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7256152	1.00[EUR][1000 genomes]
rs8106189	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9917000	1.00[EUR][1000 genomes]
rs9917034	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19084200-19107800	Weak transcription	Right Atrium	heart
2	chr19:19096200-19104000	Weak transcription	Primary B cells from cord blood	blood
3	chr19:19096400-19103600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr19:19096800-19104000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr19:19097600-19103600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:19098000-19103600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:19098000-19103600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:19098000-19103600	Weak transcription	Hela-S3	cervix
9	chr19:19098000-19103800	Weak transcription	NHEK	skin
10	chr19:19098000-19106600	Weak transcription	Fetal Kidney	kidney
11	chr19:19098200-19104600	Weak transcription	Stomach Mucosa	stomach
12	chr19:19098400-19103600	Weak transcription	HepG2	liver
13	chr19:19098600-19109800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:19099000-19103600	Weak transcription	HSMM	muscle
15	chr19:19099200-19103800	Weak transcription	Colon Smooth Muscle	Colon
16	chr19:19099400-19105400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr19:19099600-19103600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:19100200-19105800	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
20	chr19:19100400-19103600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:19100600-19103600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr19:19100600-19106000	Strong transcription	Fetal Intestine Large	intestine
23	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:19100800-19106400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:19100800-19106400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr19:19100800-19106600	Strong transcription	Fetal Muscle Leg	muscle
27	chr19:19101000-19103600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:19101000-19103800	Strong transcription	Brain Germinal Matrix	brain
29	chr19:19101000-19105600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:19101000-19105600	Strong transcription	Fetal Stomach	stomach
31	chr19:19101000-19105800	Strong transcription	Brain Hippocampus Middle	brain
32	chr19:19101000-19106400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:19101000-19106400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:19101000-19106400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:19101000-19107200	Strong transcription	Esophagus	oesophagus
36	chr19:19101000-19109400	Strong transcription	Lung	lung
37	chr19:19101000-19109800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:19101000-19114000	Weak transcription	Small Intestine	intestine
39	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
40	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
41	chr19:19101200-19106000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:19101200-19106200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:19101200-19106400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr19:19101200-19106400	Strong transcription	Brain Substantia Nigra	brain
45	chr19:19101200-19108200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr19:19101200-19108400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:19101200-19108400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:19101200-19109400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:19101200-19109800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr19:19101200-19109800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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