Variant report

Variant	rs57716250
Chromosome Location	chr19:39654519-39654520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr19:39654432-39654632	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:39653429-39659123	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39652582..39655189-chr19:39666791..39668316,2	MCF-7	breast:
2	chr19:39628877..39631480-chr19:39652977..39654703,2	K562	blood:
3	chr19:39654109..39655802-chr19:39662035..39664979,2	MCF-7	breast:
4	chr19:39652632..39654598-chr19:39881070..39883369,2	MCF-7	breast:
5	chr19:39643041..39646015-chr19:39653933..39655727,2	K562	blood:
6	chr19:39628513..39631605-chr19:39651561..39654703,3	K562	blood:

No data

Variant related genes	Relation type
PAK4	TF binding region
ENSG00000006712	Chromatin interaction
ENSG00000130669	Chromatin interaction
ENSG00000063322	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11878229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878648	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11879084	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11879196	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11879341	1.00[EUR][1000 genomes]
rs11880984	1.00[EUR][1000 genomes]
rs11881029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882129	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882955	1.00[EUR][1000 genomes]
rs16973231	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57769351	1.00[EUR][1000 genomes]
rs58626126	1.00[EUR][1000 genomes]
rs58909586	1.00[EUR][1000 genomes]
rs59303188	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60229944	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61641657	1.00[EUR][1000 genomes]
rs7246294	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7254424	1.00[EUR][1000 genomes]
rs7260015	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73551720	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73551743	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73551744	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73551749	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73551752	0.97[AFR][1000 genomes]
rs73551786	1.00[EUR][1000 genomes]
rs73553708	1.00[EUR][1000 genomes]
rs73553711	1.00[EUR][1000 genomes]
rs73553738	1.00[EUR][1000 genomes]
rs73553740	1.00[EUR][1000 genomes]
rs73553742	1.00[EUR][1000 genomes]
rs73930300	0.93[AFR][1000 genomes]
rs73933809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73933837	1.00[EUR][1000 genomes]
rs8101586	1.00[EUR][1000 genomes]
rs8111473	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	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
4	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
5	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
8	chr19:39640200-39660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:39645200-39659000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr19:39645400-39654600	Enhancers	Ovary	ovary
11	chr19:39645800-39658000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:39646600-39659000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:39646800-39659200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:39646800-39660600	Weak transcription	Dnd41	blood
15	chr19:39647200-39660400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr19:39647600-39660600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:39647600-39664800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr19:39647800-39670400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:39649000-39657400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:39649200-39656400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr19:39649200-39659400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:39649400-39659400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:39649600-39659400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr19:39649800-39659800	Weak transcription	Primary T cells from cord blood	blood
25	chr19:39650000-39657200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr19:39650000-39657200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:39650600-39657000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:39651000-39655600	Enhancers	Pancreas	Pancrea
29	chr19:39651200-39657000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:39651200-39659000	Weak transcription	Thymus	Thymus
31	chr19:39651600-39656400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr19:39651600-39657000	Weak transcription	Fetal Brain Female	brain
33	chr19:39651800-39655000	Strong transcription	Fetal Intestine Small	intestine
34	chr19:39651800-39655400	Weak transcription	Liver	Liver
35	chr19:39651800-39656400	Weak transcription	Fetal Muscle Leg	muscle
36	chr19:39651800-39660600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr19:39651800-39660800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr19:39652000-39656200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr19:39652000-39656200	Weak transcription	Colonic Mucosa	Colon
40	chr19:39652000-39656400	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:39652000-39656600	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:39652000-39657200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:39652000-39657600	Weak transcription	NHEK	skin
44	chr19:39652000-39658400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr19:39652000-39659600	Weak transcription	NHLF	lung
46	chr19:39652000-39660400	Weak transcription	Adipose Nuclei	Adipose
47	chr19:39652000-39660600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:39652000-39660800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:39652200-39655000	Weak transcription	A549	lung
50	chr19:39652200-39656400	Weak transcription	Brain Cingulate Gyrus	brain

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