Variant report

Variant	rs9676643
Chromosome Location	chr19:39346923-39346924
allele	C/T
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	PAX5	chr19:39346908-39347353	GM12878	blood:	n/a	n/a
2	PAX5	chr19:39346785-39347444	GM12878	blood:	n/a	n/a
3	PAX5	chr19:39346923-39347301	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39346827..39349071-chr19:39352230..39353984,2	MCF-7	breast:
2	chr19:39340086..39344915-chr19:39346091..39351622,11	MCF-7	breast:

Variant related genes	Relation type
HNRNPL	TF binding region
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2318461	0.92[ASN][1000 genomes]
rs55797435	0.80[AFR][1000 genomes]
rs60286661	0.88[ASN][1000 genomes]
rs60524963	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73930211	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8111670	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911673	chr19:39335274-39365401	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39343600-39348200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:39343600-39359800	Weak transcription	Small Intestine	intestine
3	chr19:39343800-39347200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:39343800-39347200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:39343800-39347400	Weak transcription	Primary T cells from cord blood	blood
6	chr19:39343800-39347400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:39343800-39347800	Weak transcription	Fetal Thymus	thymus
8	chr19:39343800-39348200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:39343800-39348200	Weak transcription	Esophagus	oesophagus
10	chr19:39343800-39348200	Weak transcription	HSMMtube	muscle
11	chr19:39343800-39352400	Weak transcription	HUVEC	blood vessel
12	chr19:39343800-39353000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr19:39343800-39353200	Weak transcription	Fetal Kidney	kidney
14	chr19:39344000-39347000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:39344000-39347000	Weak transcription	Spleen	Spleen
16	chr19:39344000-39347200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:39344000-39347200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:39344000-39347200	Weak transcription	GM12878-XiMat	blood
19	chr19:39344000-39347400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:39344000-39347400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr19:39344000-39347400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr19:39344000-39347400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr19:39344000-39347400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr19:39344000-39347400	Weak transcription	A549	lung
25	chr19:39344000-39347400	Weak transcription	HepG2	liver
26	chr19:39344000-39347600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr19:39344000-39347600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr19:39344000-39347600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:39344000-39347600	Weak transcription	Adipose Nuclei	Adipose
30	chr19:39344000-39347600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr19:39344000-39347800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:39344000-39347800	Weak transcription	Osteobl	bone
33	chr19:39344000-39348200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:39344000-39348200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr19:39344000-39348200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:39344000-39352800	Weak transcription	Lung	lung
37	chr19:39344000-39353000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:39344000-39353000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:39344000-39353200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:39344000-39353200	Weak transcription	Right Atrium	heart
41	chr19:39344200-39347400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr19:39344200-39347800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr19:39344200-39347800	Weak transcription	Placenta	Placenta
44	chr19:39344200-39348200	Weak transcription	Fetal Muscle Leg	muscle
45	chr19:39344200-39353000	Weak transcription	Colon Smooth Muscle	Colon
46	chr19:39344200-39356400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:39345000-39347400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr19:39345000-39353200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:39345400-39350000	Weak transcription	K562	blood
50	chr19:39346800-39347400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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