Variant report

Variant	rs56144126
Chromosome Location	chr19:19212658-19212659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr19:19212433-19212685	K562	blood:	n/a	chr19:19212569-19212580
2	NR2F2	chr19:19212349-19212696	K562	blood:	n/a	n/a
3	USF1	chr19:19212420-19212701	HepG2	liver:	n/a	chr19:19212569-19212580
4	USF1	chr19:19212431-19212708	K562	blood:	n/a	chr19:19212569-19212580
5	USF1	chr19:19212445-19212681	H1-hESC	embryonic stem cell:	n/a	chr19:19212569-19212580
6	HNF4A	chr19:19212371-19212661	HepG2	liver:	n/a	chr19:19212558-19212570 chr19:19212554-19212567 chr19:19212523-19212538 chr19:19212554-19212568 chr19:19212562-19212575 chr19:19212550-19212572 chr19:19212562-19212575 chr19:19212555-19212567 chr19:19212417-19212431

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19205430..19208047-chr19:19210402..19213309,3	K562	blood:
2	chr19:19208308..19213964-chr19:19214081..19217541,6	K562	blood:

Variant related genes	Relation type
SLC25A42	TF binding region
ENSG00000181035	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10164302	0.85[EUR][1000 genomes]
rs10221450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10221529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11549380	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28498174	0.87[EUR][1000 genomes]
rs4808171	0.87[EUR][1000 genomes]
rs4808178	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4808180	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808181	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808896	0.87[EUR][1000 genomes]
rs4808897	0.87[EUR][1000 genomes]
rs4808899	0.87[EUR][1000 genomes]
rs4808909	0.83[EUR][1000 genomes]
rs4808910	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808912	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808915	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808921	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808922	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55658345	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55678828	0.87[EUR][1000 genomes]
rs56141206	0.87[EUR][1000 genomes]
rs56159042	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56227420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60489867	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60696741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72993458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72993462	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73004898	0.87[EUR][1000 genomes]
rs73004899	0.87[EUR][1000 genomes]
rs73006907	0.87[EUR][1000 genomes]
rs73006928	0.87[EUR][1000 genomes]
rs73008923	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73008928	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73008930	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73008934	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73008939	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73008945	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73008949	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73008958	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73008960	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73010908	1.00[AMR][1000 genomes];1.00[EUR][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	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19176400-19215200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:19176400-19215800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:19176400-19215800	Weak transcription	NHLF	lung
4	chr19:19177200-19215400	Weak transcription	Colonic Mucosa	Colon
5	chr19:19180200-19216000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:19180400-19216400	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:19180400-19219800	Weak transcription	HSMMtube	muscle
8	chr19:19180600-19213600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:19180600-19245600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:19180600-19248400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:19185400-19221200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:19186800-19215200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:19194200-19214000	Weak transcription	K562	blood
14	chr19:19194600-19229400	Weak transcription	Dnd41	blood
15	chr19:19194800-19215400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:19197400-19222600	Weak transcription	GM12878-XiMat	blood
17	chr19:19199000-19216200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:19200800-19215800	Weak transcription	Right Atrium	heart
19	chr19:19201800-19215400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:19201800-19215600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:19202000-19213800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:19203000-19215600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:19203800-19245600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr19:19204800-19213800	Strong transcription	Fetal Stomach	stomach
25	chr19:19204800-19214200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:19205200-19216400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr19:19205400-19212800	Strong transcription	Fetal Muscle Leg	muscle
28	chr19:19205800-19216200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:19206400-19214800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr19:19206600-19212800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:19206600-19212800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:19206600-19212800	Strong transcription	Thymus	Thymus
33	chr19:19206600-19229600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:19206800-19213200	Strong transcription	Stomach Smooth Muscle	stomach
35	chr19:19206800-19214000	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:19206800-19215400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:19207200-19213000	Strong transcription	Spleen	Spleen
38	chr19:19207600-19215800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr19:19207800-19213200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr19:19207800-19214200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:19207800-19214600	Strong transcription	Brain Germinal Matrix	brain
42	chr19:19207800-19215800	Weak transcription	Stomach Mucosa	stomach
43	chr19:19208000-19213200	Strong transcription	Brain Cingulate Gyrus	brain
44	chr19:19208400-19216200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:19208600-19221400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:19208800-19215800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr19:19209000-19213600	Weak transcription	Placenta	Placenta
48	chr19:19209000-19223600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:19209400-19221000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr19:19210000-19216400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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