Variant report

Variant	rs268665
Chromosome Location	chr19:40919086-40919087
allele	A/C
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	SP1	chr19:40919065-40919635	H1-hESC	embryonic stem cell:	n/a	chr19:40919324-40919338 chr19:40919407-40919421 chr19:40919327-40919338 chr19:40919552-40919562 chr19:40919434-40919446
2	ZNF143	chr19:40918939-40919447	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:40919026-40919535	H1-hESC	embryonic stem cell:	n/a	n/a
4	CREB1	chr19:40919057-40919648	H1-hESC	embryonic stem cell:	n/a	chr19:40919366-40919379 chr19:40919366-40919379
5	RCOR1	chr19:40918843-40919201	K562	blood:	n/a	n/a
6	POLR2A	chr19:40918811-40919630	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr19:40918885-40919149	K562	blood:	n/a	n/a
8	TAF1	chr19:40919082-40919563	H1-hESC	embryonic stem cell:	n/a	n/a
9	RCOR1	chr19:40918848-40919131	K562	blood:	n/a	n/a
10	POLR2A	chr19:40919042-40919625	H1-hESC	embryonic stem cell:	n/a	n/a
11	CREB1	chr19:40918894-40919684	H1-hESC	embryonic stem cell:	n/a	chr19:40919366-40919379 chr19:40919366-40919379

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40911341..40916843-chr19:40917541..40922029,6	MCF-7	breast:
2	chr19:40918980..40921925-chr19:41105412..41107688,2	K562	blood:

Variant related genes	Relation type
PRX	TF binding region
ENSG00000090006	Chromatin interaction
ENSG00000105227	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10402565	1.00[AMR][1000 genomes]
rs10408716	1.00[AMR][1000 genomes]
rs10422945	1.00[MEX][hapmap]
rs183852	1.00[AMR][1000 genomes]
rs187908	1.00[AMR][1000 genomes]
rs268658	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs268660	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs268661	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs268667	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs268675	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs268681	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4150994	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9676315	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
7	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs268665	CCDC19	trans	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40910200-40926800	Weak transcription	Gastric	stomach
2	chr19:40910600-40921000	Weak transcription	Fetal Kidney	kidney
3	chr19:40910600-40922800	Weak transcription	Fetal Thymus	thymus
4	chr19:40914200-40919400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:40914400-40922800	Weak transcription	Colonic Mucosa	Colon
6	chr19:40914400-40926600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:40915400-40923000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:40915600-40919200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:40916000-40919200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:40916600-40920200	Enhancers	Primary hematopoietic stem cells	blood
11	chr19:40916800-40919800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:40916800-40921000	Enhancers	Right Ventricle	heart
13	chr19:40917000-40919200	Enhancers	Fetal Intestine Small	intestine
14	chr19:40917000-40919400	Enhancers	Left Ventricle	heart
15	chr19:40917000-40920000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:40917200-40919200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:40917200-40919600	Active TSS	Lung	lung
18	chr19:40917600-40919600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr19:40917600-40926600	Weak transcription	Esophagus	oesophagus
20	chr19:40917800-40919600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:40917800-40922800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:40917800-40923200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:40918000-40919200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:40918000-40919400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:40918000-40920400	Weak transcription	HSMMtube	muscle
26	chr19:40918000-40922200	Weak transcription	A549	lung
27	chr19:40918000-40923000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:40918000-40926400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:40918000-40926400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:40918000-40926600	Weak transcription	HSMM	muscle
31	chr19:40918200-40919200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:40918200-40919200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:40918200-40919200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:40918200-40919200	Weak transcription	Right Atrium	heart
35	chr19:40918200-40920600	Weak transcription	Adipose Nuclei	Adipose
36	chr19:40918200-40920600	Weak transcription	HMEC	breast
37	chr19:40918200-40921000	Weak transcription	Hela-S3	cervix
38	chr19:40918200-40921600	Weak transcription	GM12878-XiMat	blood
39	chr19:40918200-40922800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:40918200-40923000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr19:40918200-40923000	Weak transcription	NHEK	skin
42	chr19:40918400-40919200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:40918400-40919200	Active TSS	Brain Anterior Caudate	brain
44	chr19:40918400-40919600	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr19:40918400-40920600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:40918400-40920800	Weak transcription	Spleen	Spleen
47	chr19:40918400-40922000	Weak transcription	Fetal Intestine Large	intestine
48	chr19:40918400-40923200	Weak transcription	Psoas Muscle	Psoas
49	chr19:40918400-40923800	Enhancers	Fetal Muscle Trunk	muscle
50	chr19:40918400-40924000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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