Variant report

Variant	rs10412101
Chromosome Location	chr19:19106338-19106339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19105922-19106836	HL-60	blood:	n/a	n/a
2	CTCF	chr19:19106300-19106450	HEK293	kidney:	n/a	n/a
3	CTCF	chr19:19106220-19106370	HA-sp	spinal cord:	n/a	n/a
4	POLR2A	chr19:19106270-19106734	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:19106000-19106827	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:19104289-19106900	K562	blood:	n/a	n/a
7	POLR2A	chr19:19106100-19106937	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr19:19105884-19106909	K562	blood:	n/a	n/a
9	POLR2A	chr19:19106333-19107094	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr19:19105768-19106987	K562	blood:	n/a	n/a
11	POLR2A	chr19:19106076-19107049	K562	blood:	n/a	n/a
12	POLR2A	chr19:19106305-19106430	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:19106092-19107635	HepG2	liver:	n/a	n/a
14	POLR2A	chr19:19106099-19107024	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr19:19106197-19106986	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:19099305..19102487-chr19:19102568..19107094,5	MCF-7	breast:
2	chr19:19080045..19082039-chr19:19105020..19106814,2	MCF-7	breast:
3	chr19:19106312..19108383-chr19:19109496..19112233,3	MCF-7	breast:
4	chr19:19104797..19106786-chr19:19215223..19218180,2	K562	blood:

No data

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000181035	Chromatin interaction
ENSG00000064607	Chromatin interaction
ENSG00000269131	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10402553	1.00[EUR][1000 genomes]
rs10403808	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10404020	0.83[AFR][1000 genomes]
rs10404077	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10404860	1.00[EUR][1000 genomes]
rs10404879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405178	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405609	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406282	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406341	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406496	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407260	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407753	0.93[AFR][1000 genomes]
rs10407980	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10408567	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10409265	0.88[AFR][1000 genomes]
rs10409395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411786	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10413216	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10414535	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10415998	0.88[AFR][1000 genomes]
rs10416041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416054	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416240	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417995	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418688	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10419114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420559	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422058	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422079	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422238	0.84[AFR][1000 genomes]
rs10422813	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423129	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10426131	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13344769	1.00[EUR][1000 genomes]
rs13344835	0.88[AFR][1000 genomes]
rs13345246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28369262	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28374656	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28376498	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28380085	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28421315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28445835	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28475392	0.83[AFR][1000 genomes]
rs28477157	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28477961	1.00[AFR][1000 genomes]
rs28507927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28533991	0.86[AFR][1000 genomes]
rs28568599	1.00[EUR][1000 genomes]
rs28582808	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28619464	0.95[AFR][1000 genomes]
rs28628081	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28699197	0.83[AFR][1000 genomes]
rs28720008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35646935	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57654710	1.00[EUR][1000 genomes]
rs6511012	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7252085	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7256152	1.00[EUR][1000 genomes]
rs8106189	1.00[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:125 , 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	chr19:19098000-19106600	Weak transcription	Fetal Kidney	kidney
3	chr19:19098600-19109800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
5	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:19100800-19106400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:19100800-19106400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr19:19100800-19106600	Strong transcription	Fetal Muscle Leg	muscle
9	chr19:19101000-19106400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:19101000-19106400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:19101000-19106400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr19:19101000-19107200	Strong transcription	Esophagus	oesophagus
13	chr19:19101000-19109400	Strong transcription	Lung	lung
14	chr19:19101000-19109800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:19101000-19114000	Weak transcription	Small Intestine	intestine
16	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
17	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
18	chr19:19101200-19106400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:19101200-19106400	Strong transcription	Brain Substantia Nigra	brain
20	chr19:19101200-19108200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr19:19101200-19108400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:19101200-19108400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:19101200-19109400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:19101200-19109800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:19101200-19109800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:19101200-19110400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr19:19101400-19106400	Strong transcription	Osteobl	bone
31	chr19:19101400-19106800	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:19101400-19109800	Strong transcription	Liver	Liver
33	chr19:19101400-19113000	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr19:19101600-19106400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:19101600-19106800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr19:19101600-19107200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:19101600-19109400	Strong transcription	Adipose Nuclei	Adipose
40	chr19:19101600-19130400	Strong transcription	Primary T cells from cord blood	blood
41	chr19:19101600-19130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:19101800-19106400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:19101800-19106400	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr19:19101800-19106400	Strong transcription	Colonic Mucosa	Colon
45	chr19:19101800-19106800	Strong transcription	Pancreas	Pancrea
46	chr19:19101800-19106800	Strong transcription	HMEC	breast
47	chr19:19101800-19109600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr19:19101800-19109600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr19:19101800-19109600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:19102000-19106400	Strong transcription	H1 Cell Line	embryonic stem cell

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